1.UENO 2.TAMA
I recommend both ueno zoo and tama zoo.
http://www.tokyo-zoo.net/english/index.html
For travelers you maybe like to see zoo and something(e.g. Japanese museum)
Ueno zoo is very close to other spot like
TOKYO METROPOLITAN ART MUSEUM
http://www.tobikan.jp/access/english.html
yanesen
http://www.yanesen.net/
Ameyoko
http://www.ameyoko.net/access/
Tama zoo is bigger than ueno zoo, but it takes about 40 min. from shinjuku station by express .
http://www.takahatafudoson.or.jp/
http://www.kottouichi.jp/takahata.htm
http://chef-fujiu.com/
http://www.takaotozan.co.jp/index.php
karnavi
Japan