Don't know if your kids get on ferries much, but if not, how about a day trip out to Martha's Vineyard? The ferry ride is fun and there are beaches out there.
At Acadia, rent some bikes and ride along the carriage roads. No vehicles allowed, so it's a safe ride and you'll go by various lakes along the way. Just stay on the easier routes for your youngest one. Saw lots of families with kids the age of yours when we rode there.
Niagara Falls is a fair distance from the coast (over 700 miles from Acadia), so you'll also need to plan some stops on the way back home from there. In fact I'd skip Niagara Falls unless you have 3+ weeks for this vacation as it is kind of out of the way for a trip including Maine.