We have some regular clients who fly in from Central Asia and Russia and usually need an overnight. If they don't want to come into Manhattan, they usually stay at Fairfield Inn JFK:
http://www.marriott.com/hotels/trave...k-jfk-airport/
Fairfield Inn New York JFK Airport
156-08 Rockaway Blvd. · Jamaica, New York 11434 USA
718-977-3300
Usually we get it at about $150/night plus tax. Clean, safe, convenient shuttle and good staff.
There are other hotels in the area but I really don't see the value in them (unless you are trying to earn points).