Old Town Trolley Tours might be a good option for you. It's Hop On Hop Off and is well liked. Reviewers talk about getting a deal by paying for one all-day pass which gets a second day pass for free and a harbor tour.
With the trolley, you can select different areas to hop off over the two days, allowing for a bit of flexibility and spontaneity.
The Duck Tour is wildly popular. If you don't want to miss out on that, you could certainly still do it. There will be significant overlap in areas covered, but a different perspective.
Both of these tours are small groups in small vehicles. Big buses aren't popular for Boston tours as many of the streets are narrow.
You can also book a private tour in a vehicle (not walking). Reviews and info here: tripadvisor.com/Attraction_Review-g60745-d15…
Hopefully your hotel is very near a subway stop. You can do many interesting places on your own without walking great distances.
I don't have much direct knowledge of the tours outside of Boston, but look into the bus tour to Lexington and Concord. You could also take the commuter rail to Salem. Salem has a trolley that goes around town.