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Nakano may be worth looking, but sometimes they over price stuff that they know foreigners are after (like sailor moon and other obvious stuff) I feel like all the good finds nowadays are on Japanese auction sites though. If you go in those places not hunting for a specific thing you often come out with a neat find or two though.
Some stuff I found at Mandarake or Nakano and it was the same price on ebay so I bought it there vs having to lug it back home.