The cruise we took it wasn't bad. We did RCI's Enchantment. We got to Boston early enough we had to wait a while at the airport but could sit on the benches until we got the bus transfers. Once we got to the pier it was a fairly quick process to get checked in and on the ship.
For us the hard part cam in getting off the ship. Getting off is never a favorite part of the cruise but Boston seems to be worse than some. Because of the tightness of the location you have to get on and off from deck 2. Also, the pier area outside isn't very large. Therefore they can not let very many people off at one time. Also, at least on the day we got off, they only what seemed like 2 or 3 immigration officers for a ship of 2500 people. The ship didn't help by calling colors faster than they could get off. My advice, finad a comfortable place to sit (the walking deck for example) and be one of the last ones off the ship if you can. It might be less stessful than having to fight the crowds in getting off earlier.