We just got back from Spruce Point Inn and I recommend you stay there. Check out my review in tripadvisor. The other hotels are basically motels, so if that's what you like then I agree with the recommendations listed, otherwise check out SPI. Have fun!
The Spruce Point Inn is nice, but not really walkable to town. There are many nice inns in Boothbay Harbor. Many are right in town and most are on the water or have water views. You can check this list to get started:
I would not limit yourself to hotel restaurants if you stay in town.
We recently stayed at Harborage Inn - a nice b & b -- individual entrances, breakfast buffet which was wonderful, waterfront and close to town -- very nice without the usual b & b drawbacks.
Suggest you might consider the Thistle Inn. It is a landmark in the Harbor and has a very nice restaurant and the rooms are pretty nice for one night. I have stayed there many times over the years as has my son and his wife who live in the Augusta area One can easily walk down to the harbor area where there are numerous shops but not many open in early Winter time.
dikthai -- Glad you like the Thistle Inn, but probably won't help the Original Poster who asked the question much -- they were visiting Maine in mid-September !!
"Mainer on the go" - You are very correct but many people planning trips look at the various forum topics and I thought that my suggestion might possibly be useful by someone else. Perhaps not! But it's out there for anyones use as are all of the posts on the various TA forums. I, for one, have found so called "late" posting vey useful in my many travels thoughout the world.
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