You could certainly do the ferry at night, but you're looking at a full day to get to St. John's, NL and a full day to get back to the mainland. If you only have 2-3 weeks that will chop two days off your actual doing-stuff time.
If you had three weeks you could do a driving route along the St. Lawrence into New Brunswick to Moncton, then south to Saint John, NB which is only 100-200 km from Bangor, ME. (I'll be in New Brunswick myself in June.) Doing the north shore of the St. Lawrence would be nice but you'll need to find a ferry - there is one from somewhere in Gaspésie to Dalhousie, NB. I'm not sure about costs or timetables but you should be able to find it on google.