The US Coast Guard says there were six people on board the helicopter. Coast Guard officials say they received word of the crash shortly after 7pm local time and launched three response boats to the scene.
The FAA said the Eurocopter AS350 chopper was upside down.
The pilot had called in a emergency to the La Guardia Airport air-traffic control tower, sources told the New York Post.
"There was about a minute where we didn't see anyone come out, then after a minute we saw a man come out holding onto a raft screaming, 'Help! help! Ah!' and then inaudible screams," witness Brianna Jesme told the Post. "It was horrifying."
CBS posted video which it said showed a survivor emerging from the crash. The crash happened near East 90 St and north of Roosevelt Island. Video posted to Twitter shows a red helicopter splash down in the river.
Within minutes, the helicopter disappeared beneath the waves, witness John Magers, 24, told the Post.
"It looked like it was completely submerged," he said. "It couldn't have been any longer than 5 minutes."
Magers said he saw police drop divers into the river.
A witness told NY1, "We heard it hit the water, and then automatically, it drowned."
Her friend added, "It landed to the side, and then it flipped over, and then for about a minute and a half, no one came out of the water, so all of us immediately called 911. And then we saw one guy climb onto the raft."
Witness Mary Lee, 66, told the Post that she saw the chopper go down from her apartment window and said she "immediately thought someone was in there and not going to live — it's cold water, it was sinking really fast.
"By the time we got out here, we couldn't see it. It was under water."
The Post reported that there are only two Eurocopter AS350's registered with the FAA in the area — both to the New Jersey parent company of tour operator Fly Liberty Charters, FAA records show. Fly Liberty could not immediately be reached for comment.
Busy skies
The skies over New York constantly buzz with helicopters carrying tourists, businesspeople, traffic reporters, medical teams and others. Crashes are not uncommon.
- A crash in October 2011 in the East River killed a British woman visiting the city for her 40th birthday. Three other passengers were injured.
- A helicopter on a sightseeing tour of Manhattan crashed into the Hudson River in July 2007, shaking up the eight people aboard but injuring no one.
- In June 2005, two helicopters crashed into the East River in the same week. One injured eight people including some banking executives. The other hit the water shortly after takeoff on a sightseeing flight, injuring six tourists and the pilot.
- AP