It happened about 1:30 p.m. Sunday off Shoreham in the Long Island Sound.
The Federal Aviation Administration says the pilot of the Beech BE36 aircraft reported engine power-related problems before the crash.
Witnesses tell Newsday the two people in the plane stood on the aircraft's wings before it submerged, then clung to a nearby rock before being rescued.
Authorities say the two people were taken to a hospital for evaluation.
The FAA says it will investigate the crash.