Avoid the bus. Stay at the Four Seasons. It is right on Boston Commons, just a short walk from the finish. I tell them that I need a driver to take me as close as possible to the start by 9:30. I wake at 8:00 am, and uber picks me up at about 8:45 (along with a couple other hotel guests following the same plan). At about 9:15-9:30 he drops us off about 1/2-1 mile from start where the police have closed the roads (this varies through the years, though traffic is always surprisingly light that morning on I-90 out to Hopkinton). We then jog over to the start and find our corrals. At 10 am we are off and running back to Boston. Shortly after 1:00 pm I cross the finish, pick up the medal, and jog about 1/2 mile back to the Four Seasons. Last year, I was on a flight out of Logan at 3:00 pm (no joke, but that was a little too close for comfort), but I typically crash and stay the night, flying out early the next morning.
Main point: avoid the bus lines out of Copley if possible. For just a few extra bucks, you can get dropped off within a mile of the start. Talk to the concierge of any hotel.