Depending on how long you're staying in Boothbay Harbor, I would just go straight there, then take a boat tour. We did one at the end of the season last year and saw quite a few places we would not have seen from the road. This year we hope to do their longer river cruise toward Bath.
If traffic isn't bad, Wiscasset is a nice village to explore, especially if you like antiques.
One activity you might consider at BBH is Cabbage Island Clambakes. One feature of the activity (besides a fun meal in a beautiful setting) is a fairly extensive boat tour of the Harbor and various islands/inlets.
There are no ferries that I know of, so each peninsula you drive down, you'll have to get back up to Route 1 to continue east/north. Once you get to BBH, there are lots of interesting little places you can go right in the area:
-- take the drive around Southport Island (after crossing the swing bridge at Townsend Gut, an maybe make stops at Ebenecook Harbor (Boothbay Region Boatyard), Hendrick's Head (lighthouse and beach), Cozy Harbor, and Newagen).
-- drive out to Spruce Point,
-- drive out to Ocean Point with a stop in the village of East Boothbay
-- boat trip to Burnt Island Lighthouse
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