Investigators recovered a knife on the NJ Transit side of Penn Station that is believed to have been used in the attack.
The 17-year-old boy is charged with murder and criminal possession of a weapon in connection to the fatal slashing.
The 30-year-old man was slashed in the neck and stabbed in the back during a dispute at Seventh Avenue and West 40th Street.
Officers responded to reports of a stabbing at a residence on Travis Avenue in Elmont around 1 p.m. on Sunday.
The incidents occurred on the southbound "E" train platform at the Union Turnpike-Kew Gardens subway station around 3:15 p.m. on Wednesday.
Police say the suspect slashed the victim across the neck.