The Long Island Rail Road train derailed at Atlantic Terminal around 8:30 am (1330 GMT) on Wednesday, AFP reported.
The passengers tried to exit the train, some only to find themselves in a tunnel filled with smoke.
According to FDNY Deputy Assistant Chief Daniel Donoghue, at least 11 people were hospitalized.
"We were lucky, it could have been quite a bit worse," he said.
Some of the injured had to be brought out on stretchers.
"I was getting up from my seat and there was a loud impact and I flew forward and then flew backward," said a passenger. "It was total chaos, there was smoke on the train and we were sitting there in shock."
The cause of the accident was still under investigation.
"103 injuries reported at scene of Atlantic Terminal LIRR train derailment, all non-life-threatening," the New York Fire Department said in a tweet.
After a Long Island Rail Road train began shaking mildly, then more violently at New Hyde Park, it derailed in October 2016, leaving 29 people injured.
Nine days earlier, one person died and 100 others were injured after a passenger train crashed into a terminal in Hoboken, New Jersey, a major commuter route from New York City's western suburbs.
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