A spokesman for the mayor’s office, Eric Phillips, confirmed the fatalities on Twitter. At least one person was rescued from the water, he said.
Authorities did not immediately say whether there were other people aboard.
Video taken by a bystander and posted on Twitter shows a red helicopter land hard in the water and then tip over as its rotors slap at the water.
The helicopter, a model used by tourist companies, went down near Gracie Mansion, the mayoral residence. A small armada of rescue boats searched for survivors.
Witnesses told local media that the helicopter appeared to fill with water quickly.
“Its’ cold water. It was sinking really fast,” Mary Lee, 66, told the New York Post. “By the time we got out here, we couldn’t see it. It was under water.”
Witnesses described seeing at least one person emerge from the helicopter and wave his or her hands for help.
A Federal Aviation Administration spokeswoman said the Eurocopter AS350 went down just after 7 p.m.
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.