The pilot, Richard Vance, 33, was able to escape the Sunday night crash after the aircraft flipped upside down in the water, officials said. He was rescued by a tugboat.
The helicopter, a private charter hired for a photo shoot, went down near Gracie Mansion, the mayoral residence.
Video taken by a bystander shows the red helicopter land hard in the water and then capsize, its rotors slapping at the water.
The passengers were recovered by police and fire department divers, who had to remove them from tight harnesses while they were upside down, Fire Commissioner Daniel Nigro said.
"It took awhile for the divers to get these people out. They worked very quickly as fast as they could," Nigro said. "It was a great tragedy that we had here."
Witnesses on a waterfront esplanade near where the aircraft went down said the helicopter was flying noisily, then suddenly dropped into the water and quickly submerged. But the pilot appeared on the surface, holding onto a flotation device as a tugboat and then police boats approached.
“We noticed a red helicopter going full speed towards the water - looked very surreal. Next thing we know it’s approaching the water slowly and then it completely crashed and sunk," witness Arineah Nazarian told PIX11.
News footage showed one victim being loaded into an ambulance while emergency workers gave him chest compressions.
A bystander, Susan Larkin, told The Associated Press that she went down to see rescue boats in the river and a police helicopter circling overhead, hovering low over the water.
"You could clearly see they were searching," she said.
A Federal Aviation Administration spokeswoman said the Eurocopter AS350 went down just after 7 p.m. The aircraft was owned by Liberty Helicopters, a company that offers both private charters and sightseeing tours popular with tourists. A phone message left with the company was not immediately returned.
Nigro and Police Commissioner James O'Neill said the rescue operation Sunday took place in a 4 mph current in water about 50 feet (15 meters) deep, under challenging conditions.
The cause of the crash is unknown. The FAA and the National Transportation Safety Board are investigating.
The helicopter was recovered in the rescue operation and towed to a pier.