The Best of Tokyo for Girl Aimed Anime (From Experience)

• Nakano Broadway: a short train ride from Shinjuku, this is a large shopping complex that houses many used anime merchandise stores. I found the prices are less than Ikebukuro or Akihabara. The Mandarake (or at least the anime and manga one) has tax free shopping for tourists when you spend more than 10,000 Yen (about $90 USD) and show your passport.Aloha Toy is a neat little shop with bishounen character merch and fair pricing, it's my favorite shop in Nakano Broadway. The basement level has a small ice cream stand that you can buy a towering ice cream cone of 7 flavors, it was hard to eat by myself though!
• Otome Road (Ikebukuro): Otome Road is a stretch of stores that cater to female otaku, including a costume store, one for doujinshi, used books and cds/dvds, and my favorite one, the used character merch stores. Crowded next to each other, the two best ones are Lashinbang and K-Books. Prices can differ considerably even on the same item between the two stores, so unless you need it desperatly or it's a real steal, if you have time look at both stores and see how much the price differs.
• K-Books and Lashinbang also have locations off Otome Road but still in Ikebukuro. If you head to the giant Animate store, you will find the second hand shops across directly across from it. They are both downstairs, watch your step! There is also a store that specializes in character theme pillows that is on one of the upper floors. While the locations on Otome Road focus on idol and serious bishounen catering character merch, the basement locations have the shounen and sports series merch.
• Mandarake Ikebukuro: IF you like doujin go here. Even your rare pair probably has something. They also have a small but nice wall of used character merch. This is another one of the stores you can do the tax free deal at. (I think it was 5000 yen instead of 1o,000 too).
• Akihabara: While mostly still catering to the male gaze, and you may see more boobs and loli's than when in Ikebukuro, you can still find some goodies catering to your taste. Mandarake, one of Japan's largest used otaku merch stores, has a huge store in Akiba with 7 (or 8?) floors of anime, manga, doujin, hentai, books, movies etc. and one of the floors is dedicated to figures and merch. I've found some good stuff there, if you don't mind doing a little hunting. Recently anime overlords Animate opened a 3rd store in Akiba that sells all female gaze based anime/manga goods, I have not been yet but I look forward to seeing it when I do. Kotobukiya has a store in Akiba that has a least one floor dedicated to female based anime/game merch, like Utapri and Rejet stuff. Some of the smaller used stores around Akiba have small sections of girl oriented merch, I usually found it shoved in the back but their prices were decent (maybe they don't know about what girls will pay for enstars merch?)
• Bookoff: These are all over, but if you like/can/want to read and find cheap manga/BL/magazines/art books this is the place. The cds/dvds were still pretty pricey but that seems to just be a norm in Japan.