Originally Posted by
eternaltransit
Desk (or really, flight) will close 60 minutes before departure, so it's really up to you how fine you want to make it, considering TSA lines and your walking speed to the gate.
Of course the time waiting in the queue for the checkin also plays a part here. 4 hours seems excessively long, but then I don't know the Y checkin setup at JFK. 2 hours is my normal rule flying J (or F), and that is always ample.