I'd probably stick with the aquarium & Faneuil Hall. Maybe with a short walk up the Rose Kennedy Greenway to Columbus Park. There will be lots for your DC to see and do.
You might also consider the Children's Museum or Boston Common.
Problem is, it's hard to know what the weather will be like.
I don't know that I'd do a day trip from Maine. If you're flying in/out of Logan, I'd put it at the end of the trip - depending on how active a time you're planning for ME. Then again, if it's a quiet time in ME, then maybe it'd be nice to break it up a bit. Although the train travel would be a slog with the DC.