Tokyo and a few day trips are good enough. Day trips - Yokohama, Kawaguchiko, Hakone.
Bring them to the parks - Yoyogi Park, Shinjuku Gyoen, Showa Kinen Park (I love this one, always a lovely sight to see so many families hanging out and picnicking), Ueno Park and Inokashira Park (sakura trees).
Take the direct buses if you’re unfamiliar with the trains for some locations. If you liked shopping, there’s lots of shopping malls everywhere.
I once met up with a friend who brought his wife and his 2-yr old gal during some parts of my Tokyo trip some years back. We only managed to watch three shows (two outdoor, one indoor) and no rides in DisneySea. They did manage to take pictures with some Disney characters during greeting sessions. Didn’t do much when we were in Odaiba, we did go onto the Ferris Wheel and let the couple walk around Venus Fort while my mister and I took care of their little gal. They didn’t manage to venture much but I felt it was alright, especially when they had a young one with a stroller.