The AirTrain does not go to or from Penn Station. You will need to get from Penn Station to Jamaica Station (and back) by either the Long Island Rail Road or the "E" train subway; AirTrain will take you from Jamaica Station to the various terminals at JFK. The cost of the subway or Long Island Rail Road is NOT included in the $5.00 AirTrain fare. The AirTrain fare is payable with a pay-per-ride Metrocard, which is also usable to pay the separate subway fare. The subway will be cheaper than the Long Island Rail Road for getting to and from Jamaica Station, but it will take about 20 minutes longer in each direction.
The AirTrain does not go to