What time of year are you visiting? Boston in the gorgeous spring or summer is very different from Boston in the rainy-or-freezing winter. (Edit: OK, based on READING I assume this is mid-November.)
For someone who likes boats:
I'm a big fan of the commuter ferry from Long Wharf to the Charlestown Navy Yard. (It's just a fun boat experience, not an especially useful commute — you can go 'back' downtown with a $10 Uber ride, like 10-15 minutes, but if you need a car seat, this may not be an option.) Up there, the USS Constitution museum is fun for up to an hour or so, a bunch of hands-on stuff and very eager docents who are happy to tell you all about old timey sailor stuff. Also at the same site is an actual boat (the USS Constitution itself) which you can walk around on; it's pretty fun! This can almost all be indoors depending on the rain and it's probably one of the shortest ferry trips you can take (longer trips might go out to the Harbor Islands but eat up more of your day.)
Last edited by mherdeg; Nov 2, 2016 at 2:58 pm