Taxi is direct and fastest but could cost $80 or more. You can take NJ Transit train from NY-Penn Station to Newark-Penn Station. You will arrive at JFK too late for NYAS express bus to Penn Station so take AirTrain from terminal to Jamaica Station ($5), transfer to LIRR to NY-Penn Station ($5.75) and take any NJ Transit train that stops at Newark ($5).
Taxi is direct and fastest