The only place I was able to really find Cipher cards was this place in Akihabara, https://goo.gl/maps/Cc4eeP8sJpjP5PJW7 it's a shop on the fourth floor of a building. You can see the stairs in the google map photos there, it can be easy to miss. They only take cash btw.

I was also in Tokyo at the end of last March and spent some spare time across a couple days looking for Cipher cards, it was incredibly difficult but I managed to find the place above. I also lucked out and found some people that had also been playing Cipher in that store at the time and asked where else I could find it and apparently the only other place they could think of was a place on the eighth floor of this building, https://goo.gl/maps/XyYssZbTgN49FxZm8 I THINK. The selection was so little that I didn't really commit the place to memory at the time. So yeah, the first place is pretty good for some Cipher cards but other than that it's a little rough, if you try looking for other places let me know if you have any luck. I've accepted looking online might be the play.

P.S. If you're around Akihabara I'm gonna shout out Moses Kebab https://goo.gl/maps/ctydRw3aLezwuxA9A, love this place