The AirTrain was a breeze. Maybe three people on it. The LIRR was a little crowded but nothing too bad. And I made it to Penn station with an hour to spare so I walked around Manhattan a little and had breakfast. I took a cab back to Penn Station and almost missed my train but made it there on time .
Almost forgot... my plane was about 30 mins late (the air traffic control center in New Mexico was out - not jetBlue's fault) so I was glad I got the 10:03 train!