You could think about taking a look at Ogunquit, Maine. It's a about 1 1/2 hours north of Boston.
Once there you can easily make day trips to Kennebunkport, Portsmouth, NH and other ocean communities. There's gorgeous views and a killer beach.
You'll find many restaurants including casual outdoor places for lobster and antique shops up rte 1.
There's also a small mountain that you can hike.

http://www.ogunquit.org/aboutOgunquit.php

I think a stop in Lexington and Concorde to see where the Revolution started after all the sights you will see in Boston would make a good follow-up.

When in Acadia take the ferry over to the much less crowded Schoodic Peninsula portion of the park, rent bikes and do the loop road.

Oops, drop the "e" off Condorde in my post above. I am going to blame that on too may years in the aircraft industry.

Check out York ME for beach time. Great sandy beaches. Walk up to Nubble Light. Kids can walk around by themselves.
But, on the way, your family might enjoy the cruises out of Portsmouth NH. We enjoyed the mailboat cruise of Casco Bay/Portland ME but there's not a lot of narration. It might be a little dull for the boys. OTOH kids on the islands commute to school via the boat.
I would schedule a picnic lunch at the top of Mt Battie in Camden ME as you travel north to MDI. Don't forget the binnoculars. It overlooks a very active and beautiful harbor. You can take the auto road or hike. Camden is where a lot of windjammers are based. If you're on the right day, you would see them coming back or leaving for a week's cruise.
Depending on your schedule - Owls Head Transportation Museum might be an option. They have interesting things on weekends when some people will fly antique airplanes. Nearby is a short hike to Owls Head Light. Another great view.

It's not on your way home but you might find a similar place. In VT we found a popular swimming place on a river. On section was so shallow you could walk across (but very rock and we didn't have water shoes). Up stream there was a small waterfall, granite ledges and a deep pool.. Older kids were jumping off into the pool. We went back with a picnic lunch just to watch the fun. We have a swimming hole in our town with a big rock to jump from.

DeLorme publishes an atlas and gazeteer for each state. You can find waterfalls and covered bridges etc in it.

On way to MDI if you go Rt 1, north of Camden and before Ellsworth there's a Chicken Barn Antique place. First floor antiques. Second floor used books. They have a website.

I was born and raised in Maine and have lived in the mid-coast region since I was 9 so maybe I am biased but I think your whole family will love the Rockland area. You (Mom) will enjoy all the things on your list here and Dad can satisfy all of the things on his list too with a jaunt north to Acadia National Park (two hours). All of you might might enjoy a windjammer cruise - enjoy lobster dinner, help steer the ship and raise and lower sails, explore on your own in one of the ship's rowboats, and see scenery that most visitors to Maine miss. There are a bunch of historic tall ships in our area and one specializes in family trips - http://www.MaineSailingAdventures.com . The accommodations are small but cozy and you can choose just one night or as many as six nights. The cool thing for your family would be unpacking once and visiting multiple destinations without having to worry about traffic, restaurants, and activities. If find yourself staying in Rockland, there's plenty to do even if it rains - the boys might like the Owls Head Transportation Museum, the Maine Lighthouse Museum, or the Puffin Center. Dad might like a hike up Mt. Battie. therealmaine.com has lots of information about where to stay, where to eat, and what to do in our area.

Have fun and enjoy your trip to Maine!

DFrostNH mentions the Delorme atlases and gazeteers. Pick one up at the Delorme map store near Yarmouth http://www.delorme.com/mapstore/default.aspx and check out Eartha.

Pemaquid Point lighthouse is a pretty neat place too.

In the Bath area there is theMaine Maritime Museum, Popham Beach, and Reid State Park, both are better at low tide. Hike to Morse Mountain, take Parker Head Road to get there.

Wiscasset is a cute town, full of artsy crafty stuff with Red's Eats, an overpriced lobster roll shack right by the causeway.

We used to stay in North Edgecombe at what is now called either Sheepscot River Inn or Sheepscot Harbor Village and Resort. I suspect their prices have changed since they were called the Edgecombe Inn.

Thomas Moser probably buys his tools at Lie Nielsen Toolworks in Warren. You can visit the showroom and play with some nice tools. Their website has a link "Visit Maine" with some lodging and dining suggestions.

Someone already mentioned Pemaquid Point lighthouse, but anywhere between Freeport and Wiscasset heading south of US1 you will find cute and scenery and lobster.

We enjoyed hiking Dodge Point Trail in South Newcastle with our kids.

Mark

While the itinerary looks just fine, I would be more concerned about budget. (DAY 14 drive HALF-way back from MDI to Delaware!)

A hotel alone for 4 people in central Boston will run $300+ a night (before parking).

I would consider home rentals. More room, lower price, and not every meal needs to be at a restaurant. The result being you will AVERAGE $350-$400 per day (higher in Boston, lower in Maine).

To stay within your budget with only hotels will mean not so nice places that are farther from where you want to be in all three locations. VRBO is our families go to for vacation rentals. http://www.vrbo.com/