tons of places in Tokyo:
http://billiard-friends.net/01/15tokyo.html Here are some places I have been to:
Shinjuku:
TukTuk - you can reserve a table beforehand by phone. nice date spot/food/drinks
Suntimes - big place, below the old Liquid Room. Has 3 huge snooker tables also.
Bagus - kinda pricy but ok. 2 or 3 locations.
Shibuya:
Ohwada - lots of serious players. lots of tables.
Takadanobaba:
BigBox - lots of tables (including 3 and 4 cushion), lots of students
Sansui - old old place, dirt cheap but so are the tables
Shin-Okubo
Kobayashi - across from the station, above the pachinko parlor. mix of 3-cushion and regular tables. Sometimes pros from the Phillipines will come in to practice.
Sugamo:
Place by the station, relatively new and nice
Nakano:
King Dome - my local favorite. the only place where you will see a big fat cat sitting on the benches eyeing your play.