U.S. Coast Guard Petty Officer Erik Swanson said the victims were found inside the single-engine aircraft, which was pulled from about 30 feet of water about 11 p.m., several hours after the crash, Newsday reported.
The victims' names had not been released.
The newspaper said the plane, a Globe Swift, had taken off from Spadaro Airport and crashed about 3 p.m. EDT.
Witnesses told Suffolk police they heard the plane's engine sputter and saw pieces of the tail fly off, Newsday said.
After the plane hit the water, people in nearby vessels tried to get into the the cockpit, where they saw the two men, who appeared unconscious. They also tried unsuccessfully to keep the plane from sinking by tying a rope to it.