So I think a Duck Boat tour is pretty much mandatory.
http://www.bostonducktours.com/
The Freedom Trail is definitely a thing, and very cool. Lunch at Faneuil Hall is common (though it is stupid crowded and seating is a challenge). Visiting the oldest warship afloat, the USS Constitution, is definitely nice. Bunker Hill Monument is like a stone's throw from there, but I pretty much favor a "point at it and look" approach there. But hey, if you REALLY like stairs, go for it.
https://www.nps.gov/bost/learn/histo...e/ussconst.htm
https://www.nps.gov/bost/planyourvisit/bhm.htm
I've never been a big fan of the whole Harvard Yard thing. Doesn't excite me any, but some seem to like it.
The art museum is excellent, and if you're into it, you might also very much like the Isabella Stewart Gardner museum. The aquarium is also very good. We don't have a zoo that is anywhere near worth visiting, so forget that. Fenway Park is a common place for visitors to hit (see what I did there?) if you're into baseball.
https://www.gardnermuseum.org/
http://www.mfa.org/
The Museum of Science is as good as most you will find in big cities. JFK Library is pretty good.
If you're staying in teh city, dinner in the North End is usually something worth doing. That's the Italian enclave of Boston.
If you're in the area, Copley Square area can be a thing either day or night. Plenty of shopping (two malls connected by a skywalk, as well as shopping along the street), and a few "sights" of sorts to see.
Trinity Church
Boston Public Library
Christian Science plaza
https://www.massvacation.com/blog/20...copley-square/
https://www.christianscience.com/fin...-mother-church
And in that same area is the Prudential building, which has an observatory from one of the tallest buildings in Boston.
https://www.boston-discovery-guide.c...l-skywalk.html