"I've always liked 3D," declares Martin Scorsese breezily, his brown eyes twinkling from behind the trademark black-rimmed glasses which seem larger (and more impressively varifocal) in real life. "I mean, we're sitting here in 3D. We are in 3D. We see in 3D. So why not?" He smiles at me like it's the most obvious thing on earth, his face alive with boyish enthusiasm (even though he turned 68 last week), his well-groomed silver-grey hair lending an air of statesmanlike authority. I smile back, my heart full of anxiety about the "future of cinema" in the post-Avatar stereoscopic 21st century, wondering whether my hero would look quite so imposing wearing the 3D specs that we'll all to have to wear to watch his new movie.

Raised in Queens and Manhattan's Lower East Side, the son of second-generation Sicilian immigrants (a seamstress and a clothes presser), Scorsese grew up during the first wave of 3D, which threw up titles like House of Wax, Creature from the Black Lagoon and Hitchcock's Dial M for Murder. A somewhat sickly child and sometime altar boy, he devoured movies from an early age, declaring once that "movies and religion" had been his whole life. "That's it. Nothing else."

In the early 1970s, having served his apprenticeship under exploitation maestro Roger Corman, Scorsese revolutionised popular cinema with edgy films such as Mean Streets and Taxi Driver, inspired as much by the French nouvelle vague and Italian neo-realism, as the great traditions of British and American cinema. Although his recent movies have been far more financially profitable (The Departed, The Aviator and Shutter Island all cleared the $100 million mark at the US box office) it is these early classics which remain Scorsese's defining works, along with Raging Bull, King of Comedy and Goodfellas, all of which similarly showcased an extraordinary creative relationship with leading man Robert De Niro.

Riding the same generational wave that produced "movie brats" such as Steven Spielberg, George Lucas, Francis Ford Coppola and Brian De Palma, Scorsese made movies that had a hip counter-culture cache and (crucially) an authentic pop sensibility. "Popular music formed the soundtrack of my life," explains Scorsese, who has littered his movies with iconic rock cues, from unforgettable uses of "Jumpin' Jack Flash" and "Be My Baby" in Mean Streets to a cameo appearance by members of the Clash in The King of Comedy.In 1976, he documented the Band's farewell concert in The Last Waltz. The movie, released two years later, defined the "rockumentary" genre, and inadvertently gave birth to the ultimate rock parody This Is Spinal Tap.

In 1980 Raging Bull brought him his first Oscar nomination for best director, an accolade that would be repeated for The Last Temptation of Christ, Goodfellas, Gangs of New York and The Aviator (Age of Innocence earned a second screenplay nod). When he finally won an Oscar for The Departed in 2007, it was widely accepted that the long-overdue award was as much an apology from the Academy for failing properly to honour his past glories as a plaudit for his deft remaking of the Hong Kong thriller Infernal Affairs. As the oft-snubbed Scorsese himself said as he accepted his award: "Could you double-check the envelope?"

Growing up among "gangsters and priests", Scorsese outdid even Godfather director Francis Ford Coppola as the definitive cinematic chronicler of the American underworld with his hard-hitting movies. Yet now he is confounding expectations with an adaptation of Brian Selznick's child-friendly "historical fiction" book The Invention of Hugo Cabret – his first film to be made in 3D. Hugo Cabret has been described by Selznick as "not exactly a novel, not quite a picture book, not really a graphic novel or a flip book, but a combination of all these things". Will Scorsese's film, which reteams him with Aviator screenwriter John Logan and features (among others) Ben Kingsley, Christopher Lee, Ray Winstone and Sacha Baron Cohen, be as hard to categorise? It certainly seems so. Set in Paris in the 1920s, the tale centres on a 12-year-old "orphan, clock-keeper and thief" who "lives in the walls of a busy Paris train station where his survival depends on secrets and anonymity". An encounter with an eccentric girl and the owner of small toy kiosk in the train station sets in motion a mysterious adventure involving a stolen key, a treasured notebook, and an enigmatic mechanical man (or "automaton") – with the real-life figure of cinematic pioneer Georges Méliès providing the crucial link between inventive fantasy and historical fact.

"It's really the story of a little boy," explains Scorsese, "but he does become friends with the older Georges Méliès who was discovered in 1927, or 1928, working in a toy store, completely bankrupt. And then he was revived in a way, with a beautiful gala in 1928, in Paris. And in my film, the cinema itself is the connection – the automaton, the machine itself becomes the emotional connection between the boy, his father, Méliès, and his family. It's about how it all comes together, how people express themselves using the technology emotionally and psychologically. It's the connection between the people, and the thing that's missing – how it supplies what's missing."

This is a central preoccupation for Scorsese: the ability of cinema as a mechanical process to somehow plug into the human heart of an audience. And it is perhaps this fascination, with the interface between technology and transcendence, that is the real clue to his interest in 3D. Just as Méliès was a magician who used clockwork illusion to conjure emotional responses, so Scorsese's foray into modern stereoscopy seems ironically to hark back to the birth of cinema, and the moment when the moving image became the primary art form of the 20th century.

At the end of a tough day's filming at Shepperton studios, Scorsese seems genuinely fired up about the possibilities of the 3D format. "Every shot is rethinking cinema," he enthuses, "rethinking narrative – how to tell a story with a picture. Now, I'm not saying we have to keep throwing javelins at the camera, I'm not saying we use it as a gimmick, but it's liberating. It's literally a Rubik's Cube every time you go out to design a shot, and work out a camera move, or a crane move. But it has a beauty to it also. People look like… like moving statues. They move like sculpture, as if sculpture is moving in a way. Like dancers…"

Whether or not Scorsese can do with Hugo Cabret what Hitchcock did with Dial M for Murder and find a way to use 3D (rather than letting the 3D use him) remains to be seen. But he is clearly entranced by challenges and themes of Hugo Cabret, and says that the new technology with which he's working puts him in mind of Picasso and Braque and how inspired they were by the early cinema of Méliès and the Lumière brothers.

He describes cubism as being somehow an artistic response to the advent of cinema, pointing out that "a painting can't turn" and observing that "if you look closely at some of the portraits from cubism at the time, you'll find a portrait of a woman that is really a projector". Again and again he returns to the idea of cinema being a machine that somehow "fills the gap" in people's emotional lives, bringing flesh and blood together through the movement of celluloid through a projector. "Very often I've known people," he muses, "who wouldn't say a word to each other, but they'd go to see movies together and experience life that way."

It's oddly fitting that Scorsese is talking to me on the eve of the 50th anniversary rerelease of Peeping Tom, British director Michael Powell's controversial thriller which Scorsese has long championed, but which provoked furious outrage in 1960 for depicting a psychopathic cineaste who kills his victims with a murderously adapted camera. Able to relate to the world only through his viewfinder, reclusive cameraman Mark Lewis (Karlheinz Böhm) becomes the embodiment of what Scorsese calls "the pathology, the obsession, the compulsion of cinema", his crimes dramatising "the dangers of gazing". The destructive flipside may be of the "emotional connection" explored in Hugo Cabret. It's a compulsion that Scorsese recognises as an intrinsic element of the cinematic urge, summed up in one blackly comic line from Leo Marks's script for Peeping Tom in which one of Lewis's acquaintances mutters ominously: "All this filming isn't healthy."

"A friend of mine sent me that line on a note when we were making Raging Bull!" laughs Scorsese. "I think it was one of the cinematographers who'd just seen Peeping Tom. And there is no doubt that [film-making] is aggressive and it could be something that is not very healthy. When you make a film… there are times in your life when you're burning with a passion and it's very, very strong. It's almost like a pathology of cinema where you want to possess the people on film. You want to live through them. You want to possess their spirits, their souls, in a way. And ultimately you can't stop. It has to be done until you get to the bitter end. You're exhausted. In some cases friends might have died, in some cases they don't come back, in some cases they can't make another picture. The only thing to do is try to make another picture. It's got to be done again.

"Now, I don't mean to sound dramatic, a lot of great films are made that way. And we might not only be talking about cinema here. We could be talking about other things, too. I would think that it might apply to other art forms. But I must say, that with that passion and that power, there is pathology in wanting to live vicariously through the people."

So how does that pathology express itself in Scorsese's own films?

"Well, I think in my own work the subject matter usually deals with characters I know, aspects of myself, friends of mine – that sort of thing. And we try to work it out. By 'work it out' I mean almost like 'work it through your system'. Particularly, I think, on films like Mean Streets, or Taxi Driver from Schrader's script. And Raging Bull, especially. At the end of that film, De Niro was fine, but me – I left Jake LaMotta's character more at peace with himself than I was with myself. And I was hoping to get to that moment that he was at the end of the film. That moment where he's looking at himself in the mirror. I was hoping to get there myself. But I hadn't made it. So it's a matter of living through the cinema I think."

Living through cinema can be a dangerous pursuit, as Michael Powell found out when critics tore Peeping Tom (arguably his most personal film) to shreds in 1960, shattering the glittering reputation he had built up through pictures such as The Red Shoes, Black Narcissus and A Matter of Life and Death. For two decades, Peeping Tom disappeared from distribution, becoming what Scorsese calls a film maudit (literally, a cursed film), the fall-out of which all but ended Powell's career in the UK. For a while, Scorsese admits, he thought the film was only a rumour dreamed up by hot-headed cinephiles – a belief in which he was not alone.

It was only in 1979, when Scorsese helped to get Peeping Tom into the New York film festival, and then rereleased, that the film began to be reassessed as a modern masterpiece. Powell (who later married Thelma Schoonmaker, who has won three Oscars for editing Scorsese films) described the experience of the film's rebirth as being like hearing "the cries of a newborn baby", a fitting repayment for the cinematic inspiration that Powell had provided for the young Scorsese.

"I think I was eight years old when I first saw Powell and [Emeric] Pressburger's The Red Shoes," Scorsese remembers vividly, "and it had a very strong impact on me for many reasons: the nature of the storytelling; the images; the editing; the camera movements; the use of music – and the colour. And then I saw Stairway to Heaven [the US title for A Matter of Life and Death] on a black-and-white television, and The Small Back Room, again on TV, one afternoon when I was home sick from school. In New York, there was a television show called the Million Dollar Movie, which would show a film twice a night for a week. And so one week it would be Citizen Kane. Edited. With commercials. And with the "News on the March" sequence missing. Ha! That was the first time I'd ever seen it! Then, you know, you'd get The Third Man, with half the film cut out. But one of the films they showed was Powell and Pressburger's The Tales of Hoffmann. And it was cut down to about an hour and 40 minutes or so, black-and-white, with commercials. And it had a quality like The Red Shoes – a darkness, and a humour. But what was so interesting to me was the way the camera moved with the music. And the sense of editing. I lived in a tenement with my mother and father and my brother at the time, and if that film was on twice a night, I'd have to keep watching it. At certain point, my mother would ask: 'Is it necessary to watch that again?'"

So many of Scorsese's early movie memories are like this, with the detail of how and where he first saw a movie, as acute as his recall of the film itself. He remembers visiting "a storefront on MacDougal Street in Greenwich Village in the early 1960s" where he finally saw a 16mm Technicolor print of The Tales of Hoffmann, "gorgeous, but with the entire last sequence edited out! And people were furious!"

He talks about the difficulties of tracking down early films by David Lean and Alfred Hitchcock in the days before video made everything available, and how William K Everson would show up at New York University with a 16mm print of Howard Hughes's Hell's Angels, the making of which would inspire Scorsese's own film The Aviator, his first film to earn over $100m at the US box office.

Tellingly, he recalls the colours of his childhood as being inflected by the gaudy hues of Eastmancolor which were "very powerful, very strong and very lurid, and kind of violent in a way. What I saw growing up were those colours, when there was colour. Normally it was all hallways with single lightbulbs; it was mainly black-and-white in a way. But when it was colour, it was harsh, strong; some would say lurid. My formative years were in the 50s, when you had all those popular novels with paperback covers, and films like Raoul Walsh's Battle Cry were just splashed all over the consciousness of popular culture."

Most of all, Scorsese remembers the "curiosity and sense of completion" that drove him to seek out hard-to-find films in his youth, and the undeniable fetishism of film which underwrote that all-consuming passion. "It's interesting because the fetish ideas are all there in Peeping Tom," he says. "All the elements: the projector is correct; the lenses are right; the sprockets are correct. Even the sounds of the sprockets are correct. You do…" Scorsese hesitates, then gathers himself. "There is a point in time, many times over the years… where I've loved to hear the sound of film going through a projector. And I could tell you if it's 35mm or 16mm, you know. Now that's gone, of course... but there's a certain kind of… it's like going into a trance almost, or I should say a 'meditation' of some kind. It depends what you do with it. And it has to come out other ways. For me, it was burning to be able to express myself with cinema, and to be inspired by films."

As somebody with such a profound sense of cinema, it's surprising that some of Scorsese's recent successes have been on television, a medium which he has credited with providing "what we had hoped for in the mid-60s… this kind of freedom and ability to create another world" with the luxury of "the long form of developing character in a story". Most notably, his project for HBO, Boardwalk Empire, has become a popular and critical hit in the States. Created by Terence Winter, the writer behind The Sopranos, the show is described by Scorsese, who is executive producer (he also directed the first episode), as "an epic spectacle of American history, or culture I should say, American culture".

Set in prohibition-era Atlantic City, the series perhaps provides the missing link between Gangs of New York and Goodfellas, documenting the period in which "the good intentions of prohibition [ironically] allowed crime figures of the time to become organised – to become more powerful". Despite the rather distant historical setting, Scorsese assures me that the period is surprisingly familiar to him. "To me, it's as if we're talking now about the 1980s or late 1970s," he says. "That was like yesterday to me. The 20s in my head were always very present because my parents always referred to it: the music, the people, the clothes. I know all the songs from that period; I know all the films. We knew it all. And so it was a natural transition. But you know I really was fascinated with the idea of working with Terry Winter and these guys, and taking these characters over 13 hours, developing them, developing their story, the complications of corruption in American politics."

In the wake of the success of Boardwalk Empire, screenwriter Nicholas Pileggi has been hinting that a TV prequel to Goodfellas is also in the pipeline, a prospect which Scorsese admits "is possible. I don't know yet. But we're talking to [Goodfellas producer] Irwin Winkler about it."

Meanwhile, Public Speaking, Scorsese's new documentary about writer and commentator Fran Lebowitz (hailed by some as a latterday Dorothy Parker) premieres on American television tomorrow night. Having started her career as a columnist on Andy Warhol's Interview magazine and served as contributing editor for Vanity Fair, Lebowitz is captured in Scorsese's film in conversation at New York's the Waverly Inn and on the city's streets, holding forth on subjects ranging from gender, race, celebrity culture, smoking bans, and the election of Barack Obama. After which there'll be Living the Material World, a film about George Harrison, which continues Scorsese's longstanding interest in the much maligned rockumentary format that he helped pioneer.

As for the big screen, Scorsese's most recent film Shutter Island, a throwback B-movie bug-house shrieker featuring Gothic asylums, sinister psychiatrists, and crashing lightning storms, is being touted as a major awards contender. A thematic companion piece to Scorsese's remake of Cape Fear, the film nods its cineliterate head toward Otto Preminger's Laura, Samuel Fuller's Shock Corridor, and – I would suggest – William Peter Blatty's The Ninth Configuration. It also marks Scorsese's fourth collaboration with Leonardo DiCaprio who seems to have replaced De Niro as the director's favourite muse. When DiCaprio announced his involvement in Clint Eastwood's forthcoming biopic of J Edgar Hoover, he confessed to feeling like he was "cheating" on Scorsese.

As our interview ends, and it's time for Scorsese to introduce a gala screening of Peeping Tom to a new generation of filmgoers, I wonder whether film or TV currently presents the most creative opportunities for the director. He's clearly enamoured of the narrative freedoms offered by long-form TV drama, and seems able to get any number of small-screen projects (whether drama or documentary) off the ground without difficulty. Yet as someone who remains obsessed with the "sound of the sprockets" and the "feel of 35mm", and is still sufficiently young at heart to take a late-life leap into big-screen 3D, doesn't he flinch at all from the aesthetic limitations of the small screen? Wouldn't Boardwalk Empire, for example, be better on the big screen, in the cinemas that first fired his imagination?

"Well, you know," he smiles wryly, "it is made for what I guess you would call the small screen. But we made it like a film; an epic B-film in a way. And you know what? Those small screens aren't that small any more!"

• Peeping Tom is in cinemas now, and is released on DVD and Blu-ray on 21 November

• Boardwalk Empire starts on Sky in the new year