The skytrain can be used, and there are also loads of touts for the various bus companies that all run to grand central, penn st, times sq and the hotel district from JFK very frequently.
In my opinion, if there is more than one of you, the flat fare taxi (plus toll and tips) is the best option. The busses are about $14pp (and slow and noisy) and the skytrain is similar.ly priced but I have never used it as the station is quite a walk from the BA terminal (and by then you'll have had a dozen touts approach you for taxi's or busses etc anyway)