At that time of day, the DL departure will be at the head of the list for cancellation or hold (delay) if there is any form of traffic management program in effect (very common for the corridor between WAS and BOS, including of course the NYC area. A 2-hour ticket transfer means one hour because that is the bag check deadline at JFK and that deadline means checked, not standing in line.
It is all about your risk tolerance, but there is no way that I would risk the 2-hour transfer. If you insist on flying, take the 13:15 flight and have the train schedule in your pocket in case there are weather or other problems. You can always hop in an Uber to Union Station and then Amtrak.