The derailment at around 10:30 am (1430 GMT) happened in a tunnel on the subway system's "F" line in the borough of Queens, a few miles east of Manhattan, city transit officials said.
Shaken passengers were evacuated from the underground train with the assistance of firefighters and other emergency responders. News footage showed passengers milling about on the sidewalk after being evacuated to safety.
The incident caused major disruption to one of the world's busiest underground rail systems.
New York's is one of the largest public transportation systems in the world, with some 5.5 million rides on a typical work day.