Numerous options, of course.... and others may have different (better) suggestions.... but from what you've told us, I'd think about something like --
Day 1 -- Fly Indianapolis to Boston, pick up rental car, drive to Bar Harbor (about five hours via I-95 north from Boston to Bangor, ME; I-396 from Bangor to Brewer; US Rt 1A south to Ellsworth; ME Rt 3 to Bar Harbor -- the fastest, easiest way from Boston to Bar Harbor, getting you there as quickly as possible).
Overnight: Bar Harbor If you get into town early enough, make your first stop at the Acadia National Park Visitor's Center (on your right as you climb the hill leaving the village of Hull's Cove on Rt 3 before you actually reach Bar Harbor proper). The staff and rangers there can help you plan your Park visit to match the time available and address your "young one" concerns as well.
Day 2 -- Explore Acadia National Park -- if you didn't do it on your way into town yesterday, stop at the Acadia National Park Visitors Center...If you got there yesterday, start your Park visit..... overnight again Bar Harbor.
Day 3 -- Continue Acadia National Park/Bar Harbor visit, maybe including a side trip to one of the other local towns as well (Southwest or Northeast Harbor come to mind). Another night in Bar Harbor.
Day 4 -- Early morning start back to Ellsworth, then south on US Rt 1 to Rt 27 south to Boothbay Harbor. Along the way today, consider stops at Mt Battie Auto Road in Camden Hills State Park (on Rt 1 just north of village of Camden), Camden Harbor (easy parking with nice boardwalk and benches); and Rockland Breakwater/Lighthouse. Driving time Bar Harbor to Boothbay Harbor is about 3 hours not counting stops along the way. In Boothbay Harbor, visit the Botanical Gardens and plan an evening drive out ME Rt 96 through East Boothbay to Ocean Point -- great view of the water and sunset. Overnight Boothbay Harbor.
Day 5 -- Spend the morning in Boothbay Harbor village, then head south (ME Rt 27 north to US Rt 1, US Rt 1 south to I-295 in Topsham/Brunswick, I-295 south to I-95 to Boston). The objective is to get into Boston before 3:30PM when the evening rush hour begins. Return your rental car and use public transportation for your two days in Boston -- you don't need a car to enjoy the city and traffic, parking and driving the old city streets are not a fun experience. Overnight Boston
Day 6 -- Touring Boston -- overnight Boston
Day 7 -- Bostonn touring and flight home.
