The best way to get from Philadelphia to JFK, IMO, is to take the train. So much better than being stuck in road traffic.
The only company providing shuttle service to JFK, as far as I know is Dave's Best.
http://www.davesbestlimoservice.com/
Rates are fixed, and $60 seems like a bargain to me -- is that really what they quoted you?
A better question, did you save a lot of money by flying out of JFK rather than just flying out of PHL?