You can get to your hotel via airtrain and subway--you'll get off the subway at 32nd st. and walk a quick couple of blocks. A great tool is www.hopstop.com, will show you exactly what to do/what trains to take.
You might also want to consider a Super Shuttle van. It's about $15 one way, it's door-to-door, and if you're lugging any luggage, it's much easier. (If the subways are crowded, it will be hard for you to shove your luggage on--subways are not equipped to handle luggage.)
Cheers and enjoy!
Transport from JFK to midtown