Dining in Bar Harbor, Boothbay and Kennebunkport?
I'm with Feedme; a trip to Portland for a meal is a good idea since it's a year-round place with lots of fabulous food. However, those towns are pretty gorgeous, and there are advantages to being in a tourist town in its off season: peace and quiet, seeing where the locals really go, no traffic, winter specials at some of the places that stay open. Town Hill Bistro is a really nice place just ouside of Bar Harbor and is open weekends. I think Guinness & Porcelli's is a so-so Italian place, but they do a $19 3-course dinner on Fridays. Havana closed after New Year's Eve. McKay's is a good place to get a burger or a steak, and the wine and beer lists are pretty great.
Just a suggestion, but why not try a restaurant in Portland on your way down to K'bunkport? There are tons of good ones but top of my list is Fore Street- absolutely the best, they try to use the freshest seasonal ingred. possible- in addition to some tried and true recipes they also have dishes that are new every night. If you are a mussel lover they have a great appetizer that could almost be a meal. K'bunkport is pretty quiet this time of year but Hurricane and Bandeloupe are two good places.
All three are very seasonal communities that all but roll up the sidewalks this time of year. You'll be limited to what's open; many places close for the winter and those that remain open usually have limited days and hours.
Bar Harbor, I think both Havana and McKay's stay open year round, and both are very good. Guinness and Porcelli's is pretty reliable, too, and it has some decent winter specials.
From Boothbay, it's about 15 minutes up to Edgecomb and Bintliff's Ocean Grille (an especially good choice for brunch) or over the bridge to Wiscassett, where Mark Antony's is good choice for Italian (and you might get serenaded by the chef).
K'port and K'bunk's Lower Village: I think these are open year round: Cape Arundel Inn, fine dining overlooking the ocean; On the Marsh, fine dining with tapas-style menu in bar (closed Jan.); Bandaloop, fun and funky; White Barn Inn, if you want an ultra splurge. I'm pretty sure Pier 77 has closed for the season. You might also head up to Acadame in K'bunk's Upper Village.