Police responded to the scene at the corner of Light Street and Rombouts Avenue in the Eastchester section just after 4:30 a.m.
When they arrived, they found 23-year-old Kaiison Lewis, of Mount Vernon, with a gunshot wound who was pronounced dead at the scene.
Jermaine Johnson, 28, of Mount Vernon, was also found shot in the torso. He was rushed to Jacobi Hospital, where he was pronounced dead on arrival just after 5:30 a.m.
Police have taken a suspect into custody.
Detectives believe the two victims pulled over to commit some kind of criminal activity, the exact nature of which is still under investigation.
They say the 32-year-old suspect opened fire on the two men as they sat in their car. The suspect, who has eight prior arrests, was walking away from the scene when he was spotted by responding officers.
Two firearms were recovered from the scene, a .40-caliber handgun belonging to the suspect and a .09-mm handgun.
The suspect was being questioned at the 47 Precinct, where he was not immediately cooperating.
Detectives are reviewing surveillance video from the area to sort this out. Preliminarily, this appears to be targeted, and possible retribution for previous criminal activity.