OP, posted Yelp reviews for NYC Airporter can best be described as mix - travel time is quoted as 90 minutes, could be less. Going to Penn Station, you will be going to East Side of Manhattan - and then need to switch to a free shuttle & possibly a wait, add 15+ minutes travel time. Plus, B6 is at JFK Terminal 5 and it will be stopping at least 3 more times to pickup add'l pax (5 to 10 minutes to load/board x 3 stops) so it could take 2+ hours to get you to where you wanted to be, even on a Saturday as traffic & weather are both difficult to predict and manage ahead. http://www.yelp.com/biz/nyc-airporter-astoria?nb=1

Ditto for the return to JFK and beware that it's been known to serve LGA as a stop to dropoff & take on transfer pax to JFK, so extra travel time should be allocated.

I would still do JFK if I were in your situation, but do the AirTrain & then LIRR or subway, fast & reliable - flat rate yellow taxi JFK - NY Penn would be a backup option in case of any unforeseen "surprises"