Also, the Museum of Science in Cambridge is fun. They have laser shows set to rock music. They also have a scale model of the solar system that spreads over Boston, but starts at the museum.
The New England Aquarium is fun, and they have an Omni Theater that you might be interested in.
You could catch a Red Sox game, and find out how obnoxious Boston sports fans are. It’s something to marvel at. Before the game, you could wander though the Fens. It’s part of the Emerald Necklace, part of a system of parks designed by Frederick Law Olmstead. Lilac Sunday is held in May. It’s supposed to be a fun time.
If you want to shop or people watch, I recommend Harvard Square over Fanueil Hall. But if you’re going to the North End (the Italian district - ooh, try Pizzeria Regina for me. People rave about it, but I never made it there), you’ll be practically at Fanueil Hall, anyway, so check it out. Especially the Ben Franklin impersonator if he is there. I’ve heard he’s unstumpable.
Jillian’s used to be a cool nighttime place to go. There was a floor of pool tables and one of video games, with a lot of old classics. The video games have been taken out and replaced with a bowling alley. Remember that if somebody recommends Jillian’s to you.
If you’re thinking about renting a car, you could definitely get buy with only renting for a day or two. Almost everything is T accessible, and without Boston driving experience, you might never get where you are going if you take a car (parking sucks, too). The whole green line is generally safe, as is the blue line as far as I know. (FYI, There are four branches of the green line. Each train will have a letter - B, C, D, or E. E with a red line through it doesn’ t mean ‘not E’. It means that the train doesn’t go all the way to the end of the line. It will most likely go far enough for your purposes, though.) You should probably avoid the orange line if you don’t know where you are going (the green line parallels it through most of the interesting orange line stuff, anyway). The red line is great from Alewife Station to the JFK/Umass stop. I wouldn’t go farther than that on the Ashmont branch of the red line, and I don’t know anything about the Braintree branch neighborhoods.
Somebody above me mentioned Provincetown (P-town to New Englanders). It’s a lot of fun there, but some places there don’t open up until after Memorial Day. You might want to check ahead. And only go there if nobody in your party in homophobic. I once went when an extremely homophobic ex-navy guy was in the group, and it was mortifying. He was spewing hate speech in a place where a lot of gays and lesbians go because it’s very accepting.
sigh I miss living in Boston. All this makes me want to spend a weekend just wandering around there again.