We used the subway and bus option last time we went to New York, however we only did it on the way back so we already had a MetroCard and finding the bus stop wasn't an issue. We took the AirTrain and LIRR option on the way from the airport.
Wikivoyage says you can get a Metrocard at Hudson Newstands in the airport and there is a loophole where you can get the Airtrain to Howard Beach station, buy the Metrocard without leaving the station and then go back to Lefferts Boulevard to get the bus.
http://en.wikivoyage.org/wiki/John_F._Kennedy_International_Airport
Incidentally, you can use a similar loophole to avoid the AirTrain fee at Newark airport. There is a regular local bus from Newark Penn station which costs $1.50. If you use the PATH from Manhattan to Newark Penn station, the total cost is $4.
Wikivoyage says you can get a Metrocard at Hudson Newstands in the airport and there is a loophole where you can get the Airtrain to Howard Beach station, buy the Metrocard without leaving the station and then go back to Lefferts Boulevard to get the bus.
http://en.wikivoyage.org/wiki/John_F._Kennedy_International_Airport
Incidentally, you can use a similar loophole to avoid the AirTrain fee at Newark airport. There is a regular local bus from Newark Penn station which costs $1.50. If you use the PATH from Manhattan to Newark Penn station, the total cost is $4.
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