Bay dinner cruises probably exist, but I would think there's better food available in town. Portland has a great restaurant scene for a city its size. I would do something like a whale watching cruise and then come back for dinner.
There are lobster places everywhere. If you want a traditional "lobster pound" type place then I'd just pick one that's near where you plan to be. They are everywhere along the coast. There was one a friend said was the best in Maine, but I don't remember which it was (and everyone has a "this is the best in Maine" favorite).
Rockland is about an hour and 40 mins. I believe Boothbay is a couple hours.