Try to find something with a lenient cancellation policy and book it soon, Maine fills up in July and early August. Welch House Inn comes to mind as something that has all you're looking for.

thanks joesorce! will look into!

when we visited boothbay harbor we stayed at greenleaf inn
http://www.greenleafinn.com/index.php/main-house it was right in town and it was right near the water.we stayed in room #7 which is on the third floor and has a great view of the water.they also have the admirals quarters whis is a completly separate building.
the"LOBSTER"thing
the best place to have lobster are the lobster pounds.you can research that on the internet.think 2 one pound lobsters for $20. to get to those we had to do some driving as booth bay is isolated.beautiful country. don't forget to try a lobster roll.

Town of Boothbay Harbor is very touristy. But fun for dining and shopping nevertheless. I have been wearing my bargain sweatshirt this winter. If you want our secret place to stay just over the bridge onto Southport Island you'll find it in this report along with tips about what to see/do:
www.fodors.com/community/united-states/maine-minitrip.cfm

Bill in Boston

We always stay at Browns Wharf Inn which is really a motel. It doesn't look like much on the outside but rooms are well maintained and spotless, if a bit dated and, IMO, they have the best location in town - smack on the harbor with great views. You can walk across the foot bridge into town, about 15 min. We enjoy eating lobster outside at the Lobstermen's Coop and The Lobster Dock, both on the Brown's side of the harbor. The motel also has a decent waterfront restaurant where you can eat outside or in on the water. The motel is very popular and fills up just about every nt. Wherever you stay, get reservations now, esp if you will be there on a weekend. We like The Blue Moon for brkfst.

Thanks everyone! Will start my research!