I think the water taxi is a great idea. The link to the map with the stops is here:
http://www.bostonharborcruises.com/m...r-taxi_map.pdf and I think it is very short walk to the IC. Whale watches are great, but it does take up most of the day. If you have a short time, you might want to consider a shorter boat ride and do the Freedom Trail or take in a Red Sox game if they are in town. Kids like Faneuil Hall and the North End and also the swan boats in the public garden.