I would suggest getting the Trans Bridge bus at the Public Bus Terminal at JFK Terminal 4 (international) and purchasing a one way cash fare for 45$ (as far as I recall there is no sales agent at JFK and you will have to switch or stop over at the Port Authority-same bus line). The website is www.transbridgebus.com I used them quite often when going from PA to the Newark or JFK.Also once in A-town you can use the bus which requires exact change so be sure to bring plenty with you and dollar bills.
JFK-Allentown