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Warszawa is still around - they have a reasonably large store in Shibuya.
I'd echo exactly what hat and bread said. Shimokitazawa, Shibuya and Nishi-Shinjuku are all good.
Disk Union may be a chain but it's very good and their used prices are normally lower than smaller stores.
Be aware that finding some of the smaller stores can be difficult even with a city atlas (no street names!). I have the current edition of Record Map listing every(?) record shop in Japan - you're welcome to take xeroxes of the relevent pages. PM me if interested.
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