I went to Inokashira Park Zoo with my son. Its admission fee is 400 yen ($4.04 €3.08). There is no charge for elementary school kids. Inokashira zoo is located in the middle of Tokyo metropolitan. It takes 30 minutes by train from Tokyo station to Kichijouji station which is near Inokashira zoo. Here are the animals in Inokashira zoo. The official web site is http://www.tokyo-zoo.net/english/ino/main.html.
Capybara (the biggest mouse in the world)
Giant salamander is a special national treasure of Japan.