Need help from some local FTers... We have family visiting New England from the UK. They'll finish up their trip with a week at the Cape (Brewster), then drive to Boston to fly home (yes, on a Saturday, despite my advice

!)
Anyway, they are considering this plan (please critique):
Leave the Cape early Saturday and drive up to Boston -- either drop car at Logan and take cab or T into town, or park on the outskirts and take the T in to do some sightseeing. They have 3 kids aged 11, 10 and 6 -- so maybe activities like a Duck Boat tour, Children's Museum, MoS, Aquarium, etc. Flight leaves at 7 pm, so they have a 5 pm checkin time.
Question is, what about luggage? They're flying Virgin -- not sure how early you can check bags before a flight. If they drop off the car at Logan, is there anywhere to leave the luggage while they explore? Lockers? If they park on the outskirts, they could leave luggage in the car and return to pick it all up later -- but would there then be enough time to see anything of the city? And where would be best to do that -- Braintree? Quincy area? If they're taking 93 north, which station would be most accessible, and how long to get to Downtown Crossing? Is weekend parking/T service limited?
Okay, that's all the questions I can think of. For now... LOL. TIA for any insights you can provide -- there's nothing like a local expert for the real lowdown. ^