Depending how much money you want to spend and how much time you have to get into town.The cheapest way is the subway which since the airtrain is still not up can be accessed by a shuttle bus.A train from howard beach right into town cost $2.You can also take the Q3 bus to the F subway $2.Or you can take a bus to the jamicia train station and catch the LIRR into penn station$6.75-9.75+(depending on which bus you take to the train station and what time of day it is).You could also take the supershuttle which makes stops at all hotels and is a sharred van service which is $19+tip or a cab which will run you $35+toll+tip.
If you have any questions drop me an email...
-howie