Officials initially blamed a mechanical problem after at least 35 people were hurt, one seriously, when a Staten Island ferry struck a pier Saturday morning.
The accident happened around 9:20 a.m. ET as the Andrew J. Barberi approached the St. George Ferry Terminal.
Authorities say the vessel is the same one involved in a 2003 crash that killed 11 people at the same terminal.
The ferry runs across New York harbour between Manhattan and Staten Island.
Passenger Jason Watler, 30, of the island's St. George neighbourhood, said he realized the ferry was moving faster than usual as it approached the shore, became alarmed and began to run toward the back of the boat.
"It was not slowing down," he said. "He was going too fast."
Then he heard "a real big boom."
"I stumbled a little bit," he said. "People were screaming. People were crying."
Officials said they were unsure how much damage was done to the boat, which was still afloat.
The accident appears to be the result of a mechanical failure, said Janette Sadik-Khan, commissioner of the New York City Department of Transportation.
She said the ferry's throttle failed to engage as it prepared to dock, meaning the crew was unable to use the engines to slow down the boat.
Service on the ferry line was suspended after the accident, then restored by late morning.