Joel Zaritsky told The Associated Press he was on his way to New York City for a dental convention.
"I was asleep and I woke up when the car started rolling several times. Then I saw the gravel coming at me, and I heard people screaming. There was smoke everywhere and debris. People were thrown to the other side of the train," he said, holding his bloody right hand.
Passengers were taken off the derailed train, with dozens of them bloodied and scratched, holding ice packs to their heads.
The Fire Department of New York said 130 firefighters had responded to the derailment.
The crash was reported by the engineer, and it wasn't clear if any other crew members were among the injured, the MTA said.
Edwin Valero was in an apartment building above the accident scene when the train derailed. He said none of the cars entered the water, but at least one ended up a few feet from the edge.
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