I believe you already checked this wiki.
Rail transport in Japan - Wikipedia, the free encyclopedia
Among the private lines listed in the site, these are Tokyo related lines.
Tobu Railway *
Seibu Railway *
Keisei Electric Railway *
Keio Corporation *
Odakyu Electric Railway *
Tokyu Corporation *
Keikyu Corporation *
Tokyo Metro (Toei) *
Tokyo Metro (Eidan) *
In the wiki, Metro (subway) was shown as a company but it is actually combination of two company; Eidan and Toei.
These private lines , JR and Toden are the Railroad companies in Tokyo.
Metro (Toei ) and Toden are run by Tokyo Government.
follow the link below.
Toei Transportation Information