The incident happened on the train between Varick and Christopher streets. The No. 2 train was running on the No. 1 line.
The train stopped at Varick Street and West Houston.
A witness said one of the men meant to toss a bag of beer bottles out an open train door early. But it accidentally hit the suspect, who became enraged and fatally stabbed the men, according to the Associated Press.
The victims were both 24-year-old men who were stabbed multiple times in the torso. Both were pronounced dead on arrival at St. Vincent's Hospital. They were later identified as Darnell Morel and Ricardo Williams, both of Brooklyn.
A third victim, identified only as a 23-year-old man, suffered stab wounds to the arm and neck and is in stable condition at St. Vincent's.
Police say the victims were part of a group of as many as 10 people who got on the train at 42nd Street. At some point, a fight apparently broke out with another group. Police say that group was armed. One of them had a large kitchen knife, and the suspects jumped off the train at the station after the stabbing.
Police are investigating. No weapons have been recovered and no arrests have been made.
(The Associated Press contributed to this story.)