The 05:54 from Poughkeepsie to Grand Central Station derailed as it went into a bend in the railway line near Spuyten Duyvil station.
Reports say it was travelling faster than the speed limit in the area.
The train’s event recorder, similar to a flight recorder, has been recovered.
The National Transportation Safety Board (NTSB) sent investigators to the site with instructions to inspect the overturned cars and interpret information from the recorder.
The Federal Railroad Administration has also sent their own team of investigators.
Officials have identified the deceased as Donna Smith, 54, James Lovell, 58, James Ferrari, 59, and Ahn Kisook, 35. Three of the dead were found outside the train, and one was found inside.
NTSB board member Earl Weener said his teams would be on site for several days documenting evidence.
“Our mission is not just to understand what happened, but why it happened, with the intent of preventing it happening again,” he said.
On Monday, a second data recorder was found in the train’s rear locomotive. Earl Weener said investigators hoped to download information on the speed and settings of the train from that recorder.
Some 26,000 weekday riders on the railroad were warned to brace for crowded trains during the first morning commute after the derailment.
Train service south of Spuyten Duyvil is “suspended until further notice”, the train’s operator, Metro-North, said on Monday morning. Buses were being provided to the New York subway system.
Metropolitan Transportation Authority spokeswoman Marjorie Anders said the bend where the derailment occurred was in a slow-speed area.
The train appeared to be going “a lot faster” than normal as it approached the bend coming into the station, passenger Frank Tatulli told WABC-TV.
The speed limit on the curve is 30 mph, compared with 70 mph in the area approaching it, Earl Weener said.
An official from the Metropolitan Transportation Authority is quoted by the New York Times as saying that the train operator had reported that it was going into the turn too fast and that he had performed an emergency braking maneuver.
The operator told the first rescuers to reach the scene that he had “dumped” the brakes, according to the official, who spoke on the condition of anonymity.
Dumping the brakes is said to be a last-resort move that has the effect of slamming on the emergency brakes on all the cars of a train at once. It is usually done to avert a collision with another train or a vehicle at a grade-level crossing, the New York Times reports.
A 2008 federal rail-safety law requires commuter and freight rail lines to install systems to prevent derailing caused by excessive speed, known as positive train control, by the end of 2015.
Metro-North is in the process of installing the technology.
A section of line between the Bronx and part of Westchester County could be closed for a week or more and New York state Governor Andrew Cuomo warned commuters to expect long delays.
Metro-North serves commuters from New York City’s northern suburbs. It is not part of the New York City subway system.
The accident was the second passenger train derailment this year for the rail service, which, until Sunday, had never experienced a passenger death in an accident in its 31-year history.
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