That is a license plate reader. Or sometimes its more formally called a license plate recognition system. Basically what it does is that it takes pictures of the license plates of cars that are passing by/being passed and runs them to check if there are any hits (violations, warrants, that type of deal). Many large police departments are using this system on limited number of cars.

The strange thing about the NYPD cars is how the system is set up. Usually it is set up behind/in front of the lightbar on the roof. But for some reason the NYPD opted to have it on the trunk of their cars.