Here is a schedule for the airport bus service that can take you to Port Authority (8th ave and 42nd street) which is right by Times Square:

http://www.nyairportservice.com/manhattan_jfk.html

The subway will take over an hour from JFK into midtown but its the cheapest option ($2). Just take the 'A' train at JFK to 42nd street. I don't believe JFK has an airtrain into manhattan, just LGA and EWR. The bus service can take up to a little over an hour from midtown to get out there so allow at least that much time to get there and keep in mind it stops at all the terminals. Hope this helps.