Just to be clear, are you truly connecting on a single ticket or are you transferring between two tickets?

If the latter, do bear in mind that if you no show, B6 will cancel your ticket and you will likely need to purchase a new one if you cannot find an agent to help you out. For that reason, depending on your destination and the cost of tickets, bear in mind the risk of delays (not just at security, but CBP, as well as enroute for your arrival into JFK.

The ground time you allow is all a matter of your own risk tolerance.