Four officers and a Good Samaritan jumped into the water to rescue the two men trapped in the partially submerged, upside-down vehicle, police said.
The driver of the car, Edward Franz, 29, died after being taken in critical condition Saturday night to Huntington Hospital, authorities said.
A passenger in the car, Liam O'Mara, 20, of Huntington, was treated and released, police said.
Authorities said the car was westbound on West Shore Road about 5:28 p.m. when it crashed through a guardrail near Anoatok Drive, flipped over and went down an embankment into the harbor, police said.
Ken Cochrane, chief of the Huntington Fire Department, said he and 35 of his men responded to the scene, along with Suffolk police.
Before his firefighters arrived, Cochrane said the Good Samaritan had freed O'Mara by smashing out a window with his fist.
Franz was unconscious, Cochrane said, and it took about five minutes to remove him from the vehicle. He was in back of the car, against the rear window.
To reach him, the first responders used a hydraulic prying tool to remove a door from the vehicle.
Recalling the rescue, he said: "The adrenaline is running at that point, full steam, to get that person out of that car."