If you have a lot of extra time, definitely take the Silver Line; you'll get a slow motion tour of the most boring parts of Boston, and you might sort of feel like you're in a big non-posh limo because you may well be the only passenger onboard.
If you do want the quickest route, just walk a couple blocks to the Aquarium stop and hop the Blue Line two stops to the airport right away. Theres a reason the Blue Line is crowded and the Silver Line is empty.