Yes that is it. We took the 2:45 and caught the sunset on the way back. It is really a ferry of sorts. They off loaded a car on one island. It is a great way to see Casco Bay. There is a wine and beer store across the street.
In Boston I would look at hotels around the Copley/theater district. Close to common and easy to get around on the Green line.
We always stay in York Beach in Maine at family property so don't know much about lodging in the Portland area. I would recommend renting a car. Maine coast is beautiful and just driving around exploring is what I like to do. Portland is a great town with a good food scene but I don't know if it the kind of town to stay put in.