JetBlue TrueBlue - Recommendations on visit to NYC

A coworked of mine is planning a trip to NYC soon on jetBlue and she asked me about hotels in NYC (specifically Manhattan) since I am the resident jetBlue geek ... despite having flown through JFK many many times, I have never been outside of JFK.

Can anyone make any recommendations on hotels that are convienent to Manhattan but are reasonably priced (by NYC standards) and not crappy? Do any hotels in Manhattan run shuttle service to/from JFK?

I already found a pretty good page with the options for getting from JFK to Manhattan and gave it to her should a hotel shuttle not be an option.

Thanks in advance for any advice.

I can't recommend any specific hotels from my own experience, but anything near Penn Station would be very convenient to JFK with the Long Island Rail Road connection to AirTrain. Downtown/Lower Manhattan might be slightly less expensive and the A train also connects with AirTrain JFK.

Bill