Five cars went off the tracks about 7:20 a.m. EST in the Spuyten Duyvel section of the borough,
The train, traveling from Poughkeepsie, N.Y., to Grand Central Station, was rounding a curve about 100 yards from its next stop when the cars careened off the track toward the Hudson River.
Three people died when they were ejected from the Metro-North train as it twisted and turned off the track, officials said. The fire department said 11 people were critically injured and six suffered serious injuries.
"It's obviously a very tragic situation," New York Gov. Andrew Cuomo said.
The train operator, who was among those injured, told investigators he applied brakes to the train, but it didn't slow down, a law enforcement official on the scene told CNN.
National Transportation Safety Board Chairwoman Deborah Hersman said investigators would look at the track condition, signal system and human factors in determining the cause, CNN reported.
Fire Commissioner Salvatore J. Cassano said there were about 100 people on the train, The New York Times reported. "On a work day, fully occupied, it would have been a tremendous disaster," Cassano was quoted as saying.
"I was at my desk at my computer, and I thought a plane was coming in," a witness told WCBS-TV, New York. "I jumped away. Then after the noise stopped, I looked out the window and saw the train derailment, and I called 911 right away. They put me on with the fire department. I told them what had happened, where it was, so on and so forth. ... I told them there wasn't any flames. There was a little bit of smoke coming out from one of the cars, and they got here pretty quickly."
Councilman G. Oliver Koppell, who represents the area where the train derailed, said it was "certainly the worst one on this line," the Times reported.