Try the NewYorker. Its opposite Penn Station and very easy to get to using the Subway from JFK ( generally quicker than buses/taxis, a lot less stressful and you don't get ripped off ). Its not the newest hotel in NYC but good enough and a good location for the subway. Email the hotel directly on 'reservations@nyhotel.com' for rates ( I got USD 87.50 + tax in May ). Its also worth checking their website for offers at <a href="http://www.newyorkerhotel.com/" target="_blank">http://www.newyorkerhotel.com/</A>.
PJ