JFK is not that close to Manhattan, but you have some free time. (remember you have to be back 2 hrs prior to departure). You can take the Air Train to the NYC Subway and then take the A train toward Manhattan (Uptown) this will take you about 1 hour and 1/2. You can get off at Fulton street station OR Wall street subway station and see the location where the Twin Towers used to be at, and a little shopping at Centry 21 outlet. You can also continue on the Subway and get off the Times Square or 34th treet etc...it all depends on what you want to see while you are here. The subway, you have to buy a metro card, each trip is $2.25 and the Air train costs $5.00 one way. You can use Hop Stop website or the MTA website to plan your trip. They have daily planners allowing you to input your departure area (JFK) to any location in manhattan. This is the website. http://tripplanner.mta.info/MyTrip/ui_web/customplanner/tripplanner.aspx
JFK is not that close to