take the monorail to odaiba anf look at the gundam statue. The miraikai museum is also quite neat.

Sunshine City in Ikebukuro has one of the largest gashapon arcades in existence.

There's a free projection show at the Tokyo Metropolitan Government Building in Shinjuku. It was a lot of fun. When I was there last they were doing Godzilla, Gundam , and Blue Lock. They project the video right onto the government building. There's also a free viewing platform.

Meiji shrine is nice, you can daytrip to kyoto and see the bamboo forest or golden temple. Fuji may not be open for hiking yet but you could go soak in one of the onsens at the base of it.