I often fly B6 out of JFK early in the morning and I check bags. When you do on-line check in, make sure to use "JFK Bag Drop" if you checking bags, this will speed the process of dropping off your bags (there is a special "bag Drop" sky cap station at the curb).

Even when T6 is a madhouse security never seems to take more than 10 minutes, so you should be fine.

The only other slight potential wrinkle is if your flight ends up at one of the temporary gates, then you'll have to take a 30-second bus ride to the temporary terminal.

You should be fine.