Every time this topic comes up on another travel forum in which I participate, it seems that MIA-FLL is the shortest U.S. domestic route. It's under 30 miles.
As to the shortest route served by a full jet, I believe it's COS-DEN, in which some service is on a 757. Or is DCA-BWI served by a full jet?
As to the JFK-LGA service, I'm not so sure that's served by air. Can you confirm this? Some carriers offer ground service and assign a flight number and offer 500 FF miles. ABE-EWR is one such route served by CO.