[evanelias]

AirTrain fare is $5, not $8. If you're referring to the $7.75 amount listed on their web site, that's including $2.75 subway fare since it assumes you're coming from midtown.

If you use a pay-per-ride metrocard, this can be used for AirTrain. It's only the monthly unlimited that does not.

The E train isn't the only option; the A train connects to AirTrain, as does the J/Z. But personally I take the LIRR -- it's more expensive but much faster and more pleasant. At rush hour it's typically faster than a cab, and more reliable / less variance in travel time.

Yes, you're technically correct that there's no one-seat ride to your terminal. But this is the case in some other cities as well.