To get to LGA for that flight you'd probably have to leave at 5 - so is there an Acela train that leaves around 5:30 or 6? If so, I'd take that. They can run late, but usually that is less than half hour, v. risking a flight this time of year when thunderstorms routinely build and severely disrupt air travel.

There shouldn't be a traffic problem from train station to inner harbor, although you might check the baseball schedule to make sure there isn't a home opener.