Boothbay was great. We enjoyed the ride North from Manchester, NH. My Mom wanted to stay in Bar Harbor, but with just a weekend, we decided to base in BBH. McSeagull's and Lobster Dock were really good. Brown's Wharf was where we dined our first night, but it was just ok. We LOVED our accommodations at Topside Inn. Highly recommend it, if you do choose Boothbay.

http://www.topsideinn.com/

We stayed in Rockland last summer at Berry Manor Inn. It was wonderful - free homemade pie and ice cream 24/7~
http://www.berrymanorinn.com/

Eat here [often, but check the days as they aren't open everyday]
http://www.watermansbeachlobster.com/

I think Camden is a nice central spot from which to take daytrips. Boothbay requires a little more traveling to get anywhere else and back. Just do a forum search for Camden Maine and several water-view places to stay will pop up. We enjoy the quiet High Tide Inn just outside of Camden, but it is a bit rustic and barebones.

So did you want one place to stay, or were you interested in stopping at various places up the coast?

I think it would be easier if we stay in one place since we only have 3 days. We are driving from the Cape
and we fly out from Boston.

Although I was thinking we should stay in one place - we want to see as much of the coast as we can in the 3 days. I figured we could get as far as Boothbay without spending the entire time driving???? But maybe its better to stay 2 nights in one place and then another night somewhere else. We have a early evening flight out of Boston so we have the day to drive back to the airport. We will leave the cape early Sunday morning - then Sunday night through Tuesday night on the coast of Maine- driving back Wednesday to the airport

I think the drive is so long from the Cape and since you want to see the southern coast, you might spend Sunday night south of Portland then head up to Boothbay or Rockland the next day for 2 nights. Camden can be a day trip from there. I wouldn't go further north with such a short amount of time. I would be tempted to spend the first night in Portland because of all the restaurants and Old Port area to explore. It's a city but a different experience after spending time on the Cape.
Mid-June is just about the time wild lupine is in bloom. There's a lot in some areas. Further north they have a lupine festival but it's on the weekend.