The hotel we stayed at in Japan was in a section of Tokyo called Ochanomizu. It was in between the Akihabara train stations and the Ochanomizu station. We used both, but the Ochanomizu station was the one that we used a bit more often. This particular Disk Union was right across the street from the Ochanomizu station and was only 4 blocks or so from our hotel. Though I only got to go in once, it was always cool that I was walking by my 'local' record shop every time I went somewhere.
Like the Disk Union in Nakano, the Ochanomizu station was something of a one stop shop kind of place. Most genres were represented at least a little bit. There were more CDs than vinyl, but the vinyl section was still pretty big, especially the 7" section which was well stocked with cool used records. The day we went was our first full day in Japan so I think, like in Nakano, that I probably should have tried a bit harder to get back to this shop during the trip for a lengthier dig. I have a feeling there were probably some undiscovered gems floating around, but we were tired and we hit this store towards the end of the day.
I only picked up one record here, an old four way split 7" that had a Husking Bee song on it. A cool record for sure, but I think there probably was more here to find if I had a bit more time.
Bonus Store: A couple of blocks away, still in Ochanomizu is a 2 story Disk Union store that specializes in heavy metal. I didn't totally realize that until we had gone inside and since I don't really listen to any heavy metal, we didn't stay long and I didn't buy anything, but I still think it is neat that a store like this exists and was full of people looking for some loud screeching riffs.