TokyoRobot Shop Tokyo, or also known as Tsukumo Robot Kingdom. A bit of a challene as from the outside the shop is located in a non-discript building in Akihabara. During my visit to Japan, this was hands down the most impressive shop of them all, having a nice collection of robots, kits, but also parts (ranging from electronics and mechanics like hard to find omni-wheels in all possible sizes). Very impressive. The shop is not that big actually, but when walking around you get the feeling these guys really know what they are doing.
Robot Aisle Tokyo This shop is like the others an RT-shop, and has some nice kits that could not be found elsewhere as far as I have seen. The shop also has an assembly space where staff can help you work out your challenges. The shop is quite small, but when you're in Akhibabara, it's close to the other two shops mentioned here. It's actually below the railway tracks, in a small shopping mall named Radiocenter, but not to be confused with the radio department store mentioned below. You can find other electronic components shops in this mall as well. See Google maps below to locate is.
Tokyo Radio Department Shops This is not a robot shop, but still an amazing place for electronics parts. It is a 4 story shopping mall. This beats all internetshops to be honest. It's located in the same street as the robot shop mentioned earlier. Note that there's another shop called Radio Store which is completely different and not that special.