The owner of a trendy Harlem cafe that was used as a hangout by allegedly corrupt NYPD bosses was indicted Friday for operating a multimillion-dollar Ponzi scheme, officials said.

Hamlet Peralta, who regularly entertained the high-ranking officers at his since-shuttered Hudson River Cafe, was arrested in Macon, Ga., and charged with wire fraud by federal prosecutors in Manhattan.

He is accused of swindling a dozen investors — including two businessmen at the center of the FBI’s police corruption probe — out of more than $12 million, claiming he would sink their money into a wholesale liquor business.

“As alleged, Hamlet Peralta solicited investors for his fictitious wholesale liquor business by peddling wholesale lies,” said Manhattan US Attorney Preet Bharara.

Jeremy Reichberg, a prominent figure in Brooklyn’s Borough Park, and Jona Rechnitz, an Upper West Side real-estate businessman, invested more than a million dollars in the scheme, sources said.

The pair are suspected of giving lavish gifts to NYPD officials in exchange for favors — an alleged pay-to-play scheme that sources said was brought to light during an investigation into Peralta’s liquor business.

So far, four high-ranking NYPD members have been disciplined as part of the FBI probe, including Deputy Chief David Colon and Deputy Chief Michael Harrington, who often hung out at the Hudson River Cafe. The eatery closed in 2015.

“It was a clubhouse for the bosses,” said a police source familiar with the situation. “You have a lot of bosses worried about Peralta and what he could tell the feds about what was going on there.”

A number of police parties were held at the Hudson River Cafe and Deputy Chief Colon had a relationship with Peralta, sources said.

Several years ago, Colon was trying to create his own organization called “hispanic executives reaching out,” and held at least one party at the Hudson River Cafe, with police executives and some police officers in attendance.

In July 2014, Peralta was arrested for punching a man in the face inside an apartment on East 51st Street. Peralta allegedly hit the victim so hard that he lost hearing to his left ear and suffered cuts to his face.

Former Chief of Department Philip Banks III, also under federal investigation, frequented the eatery as well, along with a pal, Inspector Ruel R. Stephenson, former head of the 30th Precinct. Stephenson has not been named as a target of any probe.

Peralta, 36, was arraigned before a magistrate judge in Macon on Friday, and US marshals were set to bring him back to New York, officials said.

He started the liquor scam around July 2013, telling potential investors he was approved as an exclusive wine distributor to a major national restaurant-supply company that was starting a wholesale wine business, prosecutors said.

Peralta claimed he owned another business called West 125th Street Liquors, when his sister actually ran that company.

He promised a 4 percent return to one investor who put up more than $3.5 million, but in reality he spent less than $700,000 on wholesale liquor, prosecutors said.

Instead, Peralta allegedly spent hundreds of thousands of dollars on debts to other investors — and himself.

“Investors’ money was also used to pay numerous personal expenses such as restaurant bills, high-end clothing purchases, gas, and spa treatments,” the complaint said.

The $3.5 million investor met Peralta in 2010 after spending time in his cafe.

“He eventually became friendly with Peralta,” the indictment reads.

A person listed only as a “recruiter” in the criminal complaint solicited money from ­another backer who ended up sinking more than $5 million into the liquor scheme.

One investor was Reichberg, a police buff who bragged of his ties to cops, sources said.

Reichberg was especially close to Deputy Inspector James Grant, who was stripped of his badge and gun Thursday as part of the ­escalating investigation.

Grant allegedly escorted Reichberg from the airport in exchange for diamonds for his wife.

Grant’s mom, Lorraine, insisted he’s not guilty.

“He is an excellent father and an excellent officer,” she said over the phone. “He’s always been a model citizen. Everybody loves him.”

Peralta now faces 20 years in prison.

“As I’ve said before, the business of our public-corruption unit is corruption, and right now business is a-boomin’,” Bharara said at a New York Press Association event in upstate Saratoga Springs.

Bharara told reporters at the event that his prosecutors sometimes rely on news stories to sniff out crooked elected officials.

The Post was the first to break the news of the NYPD scandal.

“We don’t know where all the corruption is happening, and it turns out it’s often the case you folks are better at figuring those things out. You folks can ferret out and expose things often before we can,” Bharara said.

Additional reporting by Lorena Mongelli, Kirstan Conley and Rich Calder