You are a bit late to the party sadly. Prices are high across the board, console, dos pc, pc98 etc
Used to be BOOK-OFF, HARD-OFF, JUNK-OFF, HOBBY-OFF can have some real goodies but definitely not near central Tokyo.
I was there 1 month ago and saw tourists rushing to anywhere famous for retro stuff and looking very disappointed.
I remember being amazed at some of the great stuff available back in 2014/2015 but that boat has sailed unless you go to a much more remote location.
Yahoo auctions/mercari delivered to your hotel might be an option if you plan to stay a while.
If you are into electronics I recommend the Akhibara Radio department stores for a browse though. This is one of the entrances:
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And inside they did have a tiny computer junk ジャンク shop. I took this photo to show how well known the retro value of (Dos) PC components are. Considering how tightly packed those shops are, taking up half the shop floor was this display (not for sale) and next to lots of stuff from the core duo era that was for sale...
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Cool catalogue that might interest people, no idea if it's still going
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