Base Cafe
http://www.organic-base.com/topic/index.htm

MAP - Kichijoji Station

Haven't seen this in any English websites, opened March 2007.

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Kichijoji seems to be a really good place to go for Vegetarian Cafes and quirky restaurants.

It's on the Chuo Line West of Shinjuku and a visit to Takao Mountain could be combined with a stop here.

Monk's Foods - http://www.bento.com/rev/0966.html

Soybean Farm - http://www.bento.com/rev/1113.html

not vegetarian, but there's a Thai Approved place for Thai cuisine place here: http://www.peppermintcafe.com/