Firefighters and emergency rescuers swarmed the scene near Spuyten Duyvil station in the Bronx, city's northernmost borough, where at least two bogies were turned on their sides, CNN reported. One car was just feet away from the Harlem river.
Three of the dead were thrown "as the train came off the track and was twisting and turning", the news channel said citing New York Fire Department Chief Edward Kilduff.
The train travelling from the Hudson Valley town of Poughkeepsie, 100 miles north of New York, to the city's Grand Central Station, derailed just as it was coming around a sharp curve shortly after 7 a.m., fire officials told CNN affiliate WCBS. Of eight train cars, seven were off the tracks.
Police divers were in the water hours after the crash looking for survivors, and cadaver dogs searched the wreckage.
Authorities believe all the passengers have been accounted for, New York Governor Andrew Cuomo told reporters.
It was unclear how fast the train was travelling and how many passengers were on board.
"In terms of causes, we don't know exactly what happened," Cuomo said. Federal investigators from the National Transportation Safety Board were headed to the scene, he said.
Injured were taken to several hospitals in New York.
Service was suspended Sunday on part of the Hudson Line, Metro-North said on Twitter. Amtrak said it was suspending service between New York and Albany indefinitely after the derailment.
The White House released a statement saying President Barack Obama had been briefed on the tragedy by Lisa Monaco, assistant to the President for homeland security and counterterrorism.
"His thoughts and prayers go out to the friends and families who lost a loved one and everyone affected by this incident," the statement said. "The White House will continue to stay in contact with the federal, state and local partners as they respond to this event."