McCoy's second touchdown of the game -- his 19th this season -- broke the Eagles' club record for scores in a single season. His game-ending total of 20 is the most in the NFL this season.
The running back finished with 102 yards on 18 carries.
Michael Vick threw for 274 yards and a touchdown as Philadelphia (6-8) remained mathematically alive for an NFC wild card berth.
Brent Celek made five catches for 156 yards and a touchdown for the Eagles, and Jason Babin recorded three sacks, giving him the NFL lead with 18.
Mark Sanchez was limited to 150 yards on 15-of-26 passing for the Jets (8-6), who fell into a tie with Cincinnati for the final AFC wild card spot.
New York hold the tiebreaker over the Bengals.