The Terminal - Harajuku (where I'm posting this from ;) http://theterminal.jp/about.html
ii Office - Ueno https://iioffice.liginc.co.jp/
Jelly Jelly Cafe - Shibuya http://jellyjellycafe.com/
Open Source Cafe - Shimokitazawa http://www.osscafe.net/en/
The Terminal is around ~$13 a day if you pay ~$20 for a year membership. Includes free soft drinks. Yea, just $20. Or you can get a monthly pass for ~$160
II Office is around ~$10 a day also including free soft drinks
Jelly Jelly is really tiny and the one time I went it was 100% full so I haven't actually used it.
Open Source Cafe is also pretty tiny. It's 2 small rooms, both hold maybe 7 people though I've seen them cram in 15+ for a meeting.
I've been to a few on the list
co-ba I signed up for a year ago. Plus, if you become a member they give you a security card and it's open 24 hours. Minus, it's pretty minimal, especially the 2nd floor. Feels like I sitting in an elementary school class.
kokemasaz feels like someone decorated their garage. Nice DIY vibe. The guy making Voxatron (http://voxatron.com) who goes by Zeb online says he sometimes hangs out there.
I guess I should mention he runs the picopico cafe (http://picopicocafe.com) in Kichijoji. It's only open 3pm to 10pm Saturday and Sunday and even then only if they haven't rented the place out (check their calendar) but, possibly because he's an indie game dev a lot of other mostly non Japanese indie game devs hang out there.
What kind of shocks me is how much more expensive co-working spaces are in SF and LA. They claim you'll get networking but they're usually > $500 a month for just an unassigned seat at an open table.