Monthly AirTrain passes available for $40 if you need to take it everyday. And 10 rides for $25. So if you need to take it often, it's more cost efficient than paying $5 every time!
Buy a $1 metrocard if you don't have one. Load with AirTran and Metro fare ($5+$2.75). If you're new to NYC, be sure to use the Citymapper app to calculate the best routes and costs through the city.
Here's what you do: get an AirTran card before you go through the turnstile ($5 when I left this tip). Then _on the other side_ of of the turnstile get a regular metro card for use in the city.
You most likely will need to use the restroom after taking the A train all the way from Manhattan to here. Bathrooms are clean and locked but asking red jacket attendant will give you access.
$5 dollars to ride the airtran into the airport from here is a ridiculous! Traveling witrh someone else? spend another 5, and catch a cab from here..faster and worth the money