Tokyo Transportation
Train Route Finder by Jorudan Co.,Lrd.
https://www.jorudan.co.jp/english/norikae/e-norikeyin.html
Tokyo Metro
Railways
JR East
To find about JR Lines in Japan, see this webpage
https://www.digi-joho.com/transportation-japan.html
Keio Line
https://www.keio.co.jp/english/
Tobu Railway
Keisei Line (Keisei Dentetsu)
https://www.keisei.co.jp/keisei/tetudou/skyliner/us/index.php
Seibu Railway
Tokyu Line (Toukyou Kyukou)
Odakyu Line
https://www.odakyu.jp/english/
Keikyu (Keihin Dentetsu)
Tsukuba Express
Subway Lines
Tokyo Metro
Toei Subway
https://www.kotsu.metro.tokyo.jp/eng/
Local Bus
Toei Bus
https://www.kotsu.metro.tokyo.jp/eng/
Kokusai Kogyo Bus
Tobu bus
Seibu Bus
Keio Bus
Nishi Tokyo Bus (West Tokyo Bus)
https://www.nisitokyobus.co.jp/