I second the Duck Tours (though, is your vacation the 18th-22nd? I know alot of places have that off this year because of Easter. I think the Duck TOurs are only on weekends- other than MA vaca week which is those dates. Wasn't sure if you were in MA or not.) FYI, it goes in the Charles River, not the harbor. As said, it is not on/off but you could go back and walk to most sites.
The nice thing about Boston is the Freedom Trail (literally a red line to follow on the sidewalk) takes you to most of the major sites. I think it might be 3 miles long, it's a reasonable walk even for kids. (Lots of stops on the way!) The USS Constitution is (free!) is a hit with all ages of kids. My son was convinced it was a pirate ship when he was younger.
We've also done Old Town Trolley a couple times (which is hop on/off).
FYI, too if you didn't know, Boston Marathon is Monday the 18th (and the Sox are home!), parts of the city will be nutty.