Geoff -
Here's how I would do it.
First day, as long as you are there, spend all day at Boothbay Harbor. It's a very good course, the hypermodern details (creeks, cliffs) have to be seen to be believed, and food/beverage are quite good, especially if the massive dining platform with long views at the non-returning turn is open. Why not after a long drive? I am almost certain that carts are required for guests.
Second day, yeah, get the boat and do a full day at North Haven. We are still talking about it fifteen years later. We had a full-service captain who took care of all the food and the ground transport. Famous quote - "Do I have a corkscrew on the boat? Yeah, I have one in every vehicle." The walk is a half mile, but I have always just stuck my thumb out. I would opt for a sunset cruise back to Boothbay in lieu of dinner on the island. You won't forget or regret this one, the sporty golf course is simply the icing on the cake.
Third day, stick with the theme and do Samoset. If you can find six caddies on a Tuesday I'll eat my hat, but the course is super walkable. It does get narrow and resort-y on the back, but you will enjoy most of the golf and all of the setting, which features by far the most oceanfront golf in Maine.
I will be in Liverpool on September 28 but call me regarding October 2.
PS - One other reason to go to Samoset is the stellar dining in Camden on the way home.