The Copley House is exactly where you want to be and it looks like a good place.
IMO theInn atSt John is too far away from the city center. Portland is hilly and the walk from town to the Inn is not desirable. You will either have to cab or have a car. I would definitely stay Downtown near the docks.
You don't get off the boat. It makes a loop around the bay and drops the mail, passengers and maybe a car off. It stays there for ten minutes then it is off to the next one. I think it is eleven stops. You just cruise and watch the boats, lighthouses, and boats go by. Then cruise in to the sunset. Bring a jacket as it gets cool late afternoon.