There are 2 good spots -- but cops are around, so maybe you can get permission from the PA's PR
department before you go:
a) by the bridge from the airtrain gives you a good view of Terminal 4 and some of the gates on Terminal 3.
b) at the end of the departure hall curb side -- right before you go inside the building -- you get an unobstructed view of Terminal 4's B gates. Very good as you may be able to take shots with the JFK
tower in the background.
Good luck and enjoy the spotting!
Wasim / Planemannyc