I can't speak for the rest of New Jersey or New York, but NY State Police and all NYC agencies also have EZ Passes. Probably antiquated toll systems that can't recognize patrol cars quickly enough, though as cashless tolling replaces more and more toll booths/plazas, they may eventually phase them out here
It could also just be to tag the car, it might not actually charge the agency. More reliable to have the same until everyone else does, then try to get the cameras to figure out what a police car is different from regular cars.
But I don't work for any NY agencies, so I can't say for certain haha