Definitely LGA.
The frequency at LGA is probably the only thing that matters if you'll be doing this regularly for business.
I think LGA flights are usually scheduled for less taxi time than JFK flights, too.
With AA, IME flights between LGA and ORD usually depart from a gate very close to an Admirals Club, whereas my last ORD-JFK flight departed from a gate in the ORD L concourse, which doesn't have a lounge. I haven't flown the route all that often, though. The LGA Admirals Club is quite nice.
With DL, you get to use the Marine Air Terminal, which is super convenient as others have said.
AA generally flies B738's and DL generally flies E175's on the route. The F seats on the 738 are a little bigger. But the 175 has 1-2 seating so you can get a single seat that's an aisle and a window if you like that.