Ok, if you want the best anime store in JP, in my opinion before anyone else gets mad, it's the Nakano Broadway shopping mall. It is filled with anime stores that have both new and used merchandise including some really rare stuff. While you are in Nakano check out the bar "Juke 80's." It's an 80's music themed bar that is a total blast. Everyone there is obsessed with western music and culture so many of them speak English. I literally have had multiple people coming up to me and going "Do you watch Friends?! I learned English watching it on Netflix!" If you are a fan of "JoJo's Bizarre Adventure" there is also a JoJo's Bizarre Adventure themed bar in Nakano. My favorite restaurant in Nakano is a steak house called "Steaktei Nakano" it has a statue of Joe Yabuki sitting out front so you can't miss it. Also, even though it's steak it's reasonably priced.
For getting to Nakano the Chuo-Sobu line hits both Akihabara and Nakano since you're going to be in Tokyo. You can also take the Chuo-Sobu to Shinjuku which is a very famous area. Kabuki-Cho is an area within Shinjuku which both Ichi the Killer and the Yakuza games heavily feature. Also, if you're looking for the best Ramen in Japan, again my opinion, check out Jiro Ramen in Kabuki-Cho. I have a meeting to go to but I'll think of other stuff, lol.
Any other anime you're a fan of? I know a bar that appears in Akagi and some other otaku hot spots like the Shrine from Tenchi Muyo, lol.