This is a good one.. I'd say take a cab but Friday at 5pm (by the time you leave the airport) there will be traffic on the Vanwyck, etc. So, the meter will continually increase as the cab sits in traffic on the VWE, and LIE.
If you decide on train (it should be 7.25 p/pax). AirTran to Jamaica, board E train to Roosevelt Ave, transfer to 7 train (towards Manhattan) and get off on 33rd and call your hotel.
If possible/better option - You can/should call your hotel to see if they can pick you up at 23rd/Ely off the E line as you won't need to transfer and makes your trip easier & faster. AirTran to Jamaica/E train towards Manhattan and get off on 23rd.