Dog Heart dog cafe in Yoyogi Hachiman is a fun experience for an animal lover - you can play with the sixteen dogs there, or take one of them out for a walk in the park. (Reservations are highly recommended.)
Some museums that were popular with my younger relatives - Drum Museum in Ueno, Fire Museum in Yotsuya, History Garage in Aomi (for automobile fans), Metro Museum in Edogawa-ku (for subway fans), National Museum of Science and Nature in Ueno (an excellent natural history museum). All listed at
Activities for younger kids - Where In Tokyo
Sunshine City Alpa in Ikebukuro has a number of attractions of interest, including Tokyo's only Pokemon Mega Store, a dumpling theme park called Gyoza Stadium, a manga-centered mini-theme park called J World, a very nice aquarium, and a 60th-floor observation deck.