Four people were presumed dead after a private plane — carrying a prominent East Hampton builder who crafted luxury mansions for Martha Stewart, Billy Joel and others — crashed into the Atlantic off Amagansett, LI, on Saturday.

Hamptons “Builder to the Stars” Ben Krupinski, 70, was feared among the dead, along with his wife, Bonnie Bistrian Krupinski, 70, and their 22-year-old grandson, Will Maerov. East Hampton police confirmed the trio were aboard the flight, along with 47-year-old pilot Jon Dollard.

All are believed to have perished in the crash, sources said.

The Piper PA-31 Navajo plane went down about a mile off shore near Indian Wells Beach at about 2:50 p.m., officials told The Post.

The cause of the crash is under investigation, but local pilot Bill Gardiner noted that the weather had turned stormy.

“There was a very nasty thunderstorm going on. It was unexpected. There were very strong downdrafts.”

The Krupinskis had owned the plane since at least the 1980s, Gardiner added.

The couple’s real-estate empire is worth a reported $150 million, and included the popular East Hampton restaurant Citta Nuova, where grieving workers and patrons gathered Saturday night in shock, some in tears.

The couple, known and loved by locals as “Bennie and Bonnie” — high-school sweethearts well known for their charitable endeavors — had been expected there for dinner that night.

Instead, the restaurant was shuttered, a sign explaining that the closing was “due to a family emergency.”

“They were generous beyond belief,” sobbed longtime employee Jeanne Nielsen.

“They were very philanthropic . . . their grandson Will had worked here for the summer in the past. He was a student at Georgetown,” she said.

“Their granddaughter, Charlotte, is 15 or 16. She was not on the plane. She was going to work here this summer.”

The family “flew all the time,” Nielsen said. “They were coming here for dinner tonight, and then going to the movies. Their plane was supposed to land at 3.”

She added, still crying, “They were together forever. They were the couple that was together ­forever.”

As for the restaurant’s workers, Nielsen said, “We’re broken. All of us.”

Cops blockading the couple’s home on Three Mile Harbor Road asked a reporter to give the family privacy.

Two bodies were ­recovered by Saturday night, the U.S. Coast Guard said.

One was recovered by an East Hampton lifeguard using a Jet Ski, and the other by the Coast Guard, an agency spokeswoman for the Coast Guard told Newsday.

A pocketbook was plucked from the water by commercial fisherman Dave Aripotch, who told Newsday he responded to the scene after mariners were given notice of the crash.

“I wish we could have got there sooner,” he said of seeing a piece of the plane’s nose in the water.

Ben Krupinski, an East Hampton native, pilot and golf lover, rose to prominence building lavish homes for Stewart, Joel and rocker Roger Waters of Pink Floyd.

He counted moguls such as Leon Black among his clients — but would pitch in and repair a broken sidewalk out of his own pocket, said those who knew him.

Fellow developer Joe Farrell called Krupinski “a legendary builder.”

“Truly a great builder that built the biggest and most expensive homes,” Farrell said. “I admired and respected him very much.

“His wife Bonnie was a Bistrian, and a huge land owner. Bonnie sold me many lots,” Farrell recalled.

“Ben used to lend me his helicopter. He was very nice to me even though we were competitors.”

Famous adman Jerry Della Femina once told The New York Times, “In East Hampton, Ben’s the star. You walk into a restaurant and everyone’s looking up and saying, ‘It’s Ben! It’s Ben Krupinski!’”

East Hampton gallery owner Terry Wallace said Ben Krupinski would often be at the controls of the plane.

“A lot of times he flies his own plane. He does a lot of things in the village,” Wallace said.

“He just finished the Ladies’ Village Improvement Society. If there’s a problem like the sidewalks, he’ll just fix it for nothing. He does a lot of things for nothing,” Wallace said.

“They’re good people.”

Krupinski was so close with lifestyles queen Stewart, “he took his plane and got her” when she was released from prison in 2005, ­Wallace added.

Local resident Bob Miller said, “It’s so sad. It was Ben and Bonnie? That’s so sad. He’s been very involved for decades. Incredibly highly regarded. He’s been a builder out here for a long, long time. I’ve never heard a bad thing about him out here.”

“We are stricken by this loss,” said Coast Guard Capt. Kevin B. Reed, commander Sector Long Island Sound.

“Our deepest sympathies go out to the families and loved ones of the two recovered individuals.”

Krupinski’s only child, Laura Krupinski, 52, is a former Wilhelmina model who once publicly accused her father of having an affair with Stewart.

Grandson Maerov had just started a job with ad agency Chandelier Creative, according to a post on his Facebook page.

The crown jewel of Ben Krupinski’s real-estate empire was East Hampton Point, a five-acre property with a 400-seat restaurant facing Three Mile Harbor.

It included a full-service marina, boatyard, 14 guest houses, a pool and tennis courts.

In 2015 he began building for Waters a 14,000-square-foot house with a swimming pool, a pool house and a sunken tennis court.

Among the properties on which Ben worked for Stewart was a cottage and a 24-room manse, for which he was said to have created a hidden kitchen-exhaust system.

In 1989, Krupinski renovated Bill Joel’s 12,000-square-foot Amagansett home.

Saturday’s tragedy was the second small-plane crash on Long Island in less than a week. On Wednesday, a World War II-era plane plummeted into the woods of Melville, killing its only ­occupant.