Rockville Center Inn (formerly the Sunrise) 516-593-1600 $111 w/ tax, free shuttle and continental breakfast
Five Towns Inn 516-371-2600 $101 w/ tax, free shuttle, pound cake, warm milk and cold coffee.
Hilton Garden Inn JFK 718-322-4448
Hampton JFK 718-322-7500
Doubletree JFK 718-322-2300
Holiday Inn Express 516-596-3000 $110 no shuttle, next to Rockville Center Inn
I've stayed at 5 Towns and Rockville Center. The Rockville Center Inn has more to do within walking distance (i.e. gym, restaurants, grocery store), but is further from the airport. Five Towns is good if you just want a bed that is close to JFK.
Also check hotwire.com for last minute rates.