It happened around 1:20 p.m. in the vicinity of West 30th Street and the West Side Highway and involved a flight owned by Zip Aviation, which operates for Blade and sightseeing services.
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The pilot was able to crash land on the river and exit the helicopter, a Bell 206 model.
Several bystanders captured video showing the moment a helicopter crashed into the Hudson River.
WATCH: Bystander captures moment helicopter went down
The helicopter was mostly beneath the water, but inflatable pontoons kept it from totally sinking.
The FDNY and NYPD managed to secure it and drag it to the side of the heliport, where it is was tethered to the pier until being hoisted out of the water.
It was loaded onto an Army Corps of Engineers barge and will be taken for analysis.
Authorities say the 35-year-old pilot had just refueled and was taking off to reposition to the customer portion of the heliport when the helicopter lost altitude and crashed into the river. "All of a sudden, he felt the helicopter go down," said NYPD Assistant Chief Stephen Hughes.
The pilot was the only person on board and was safely removed from the water by a NY Waterway Ferry, named the Gov. Thomas Kean.
NY Waterway says Capt. Adam Sciaino was carrying passengers between West 39th Street in Manhattan and 14th Street in Hoboken when he saw the helicopter go down.
"We just slowly eased our way up there, I could actually just stand there in position if I had to with the boat," said Sciaino. "I called out to him, he said OK."
This is Capt. Sciaino's second rescue in 10 years with the company.
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Deckhand Edwin Montoya deployed the Jason's Cradle rescue device off the bow of the ferry and pulled the pilot aboard.
"We put him up on the ladder, I happened to bring him onto the deck," said Montoya. "I asked him if he was OK, or if he was injured or is anybody else on the helicopter. He seems to be in pretty good condition. A little shaky, maybe a little nervous."
"It was just instinct," Sciaino said. "Just another day for NY Waterway rescues. We're right here. Edwin Montoya is an outstanding deckhand. He moved instantly to the rescue."
The FDNY says there were two non-life-threatening injuries reported, the pilot and one heliport worker who was injured while attempting to get out of the way of the helicopter as it came down. Both suffered hand and wrist injuries.
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Coast Guard crews and the FAA were also responding to the scene.
The West Side Highway was briefly closed southbound at 34th Street near Hudson Yards to accommodate emergency vehicles.
In 32 years, NY Waterway crews have rescued almost 300 people from the waters of New York Harbor, including 143 people rescued from U.S. Airways Flight 1549 in "The Miracle on the Hudson," the most successful marine rescue in aviation history.
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