Unless you stay at a PRIVATE park facility, the LongTerm run by the airport is all on the Airtrain which is totally free. The only time there is a charge is if you get off at the END Of the LINE which connects directly to the NYC Subway system (and another $2 to get on the subway, which is separate because you might be getting on the LIRR).
How to get from LongTerm to Airport --- Take AIRTRAIN