best = cab. if that's more than you want to pay, express bus is $15.00, http://www.nyairportservice.com/index.html
Airtrain from airport to Jamaica (for LIRR) or Howard Beach (for Subway A train) is $5.00 - onward fare by LIRR to Penn Station is $7.00, or by Subway is $2.00. http://www.mta.info/mta/airtrain.htm
Note that MTA buses and subway are not equipped to carry large items of luggage.
i took a cab. They queue up in the designated rank outside arrivals and then it took about 30 mins to our hotel.
You know what its going to cost and you go straight to your door, great if its late and youre tired and just want to book in and go to sleep.