The two AirTrain options are:
1. LIRR Penn Station -> Jamaica, then Airtrain. The LIRR segment requires purchasing a ticket ($8.75 peak) and does not accept MetroCard. The Airtrain segment only accepts pay per ride MetroCard ($5). It may appear that the LIRR does accept MetroCard, but they don't - actually it is an LIRR monthly pass printed on the back of a MetroCard, and only the pass side is shown to the conductor.
2. Subway A Train towards Rockaway -> Howard Beach JFK, then Airtrain. The A Train segment accepts all MetroCards ($2.25 or unlimited pass); the Airtrain segment only accepts pay per ride Metrocard ($5).
If you have luggage, #1 is going to be more comfortable and faster. If you're cheap, #2 is $6.50 less expensive, and maybe about 20 minutes longer. Both are actually pretty reliable, especially during rush hour.
About the ferry, I meant 1 hour for the round trip, not 1 hour each way.