They are young for all the historical parts but make sure you do some for you and your husband's sake!
Duck tour - my kids loved when they let them drive in the water.
Children's Museum is good - discounts Friday evenings I believe.
I think there is a carousel on the Rose Kennedy Greenway and at least one playground.
We love taking a harbor boat out on a nice sunny day and visiting the harbor islands.
Aquarium is always a hit. USS Constitution and there is some sort of Tea Party think where kids throw tea overboard.
Moving inland maybe the Museum of Science, Make Way for Ducklings statues (great photo op! Bring the book to read there) Swan boats for sure.
My older kids like the Freedom Trail in the North End especially - Paul Revere's house and Old North Church and then stopping for Italian food and pastries. Try to see a feast day procession!
http://www.bostonusa.com/includes/calendar-of-events/North-End-Feasts-Processions/29108/