How about Shinjuku Gyoen (http://fng.or.jp/shinjuku/)? It's a huge park in Shinjuku. You have to pay 200yen as entrance fee (the toddlers are free) but it's controlled by the capital so it's clean and safe.
You can bring your kids to Legoland for the creativities and Sanrio Puroland (Hello Kitty) for Kawaii! Even the adults can have fun with it! And also KidZania is recommendable too! They have an English program too.
The most famous sight in Tokyo must be Tokyo Disney Land and Disney Sea. Every child love Disney Land.
There are also many aquariums like Shinagawa Aquarium, Sunshine Aquarium, Sumida Aquarium, etc. Where your children can enjoy watching fish, dolphins, penguins, etc.
Ueno Zoo is the oldest zoo in Japan. Giant Panda is famous exhibition there.
My friend said KID-O-KID was fun.
It's a theme park for children with many kinds of toys and attractions. Only 600 yen for first 30 minutes. It will be charged time-basis.