In the Portland area there is Royal River Boat Yard. Alan Dugas is the owner and runs a tight ship. Brand new boom crane truck and travel lift. They are promt and on time. I've been at RRBY now for about 7 years and never once had any complaints, and I'm a picky SOB..;) Used to keep my boat at Finest Kind with Mark when I lived in Harpswell. Decent yard too. There are many good ones but in the Casco Bay area the only ones I'd recommend are Strouts Point, Finest Kind, Royal River Boat Yard, Brewers South Freeport & Maine Yacht Center.
Compared to many areas Maine has some great yards to choose from, most with very highly skilled workers.