Most of the interesting stuff is in the little shops in the bizarre. All the glass fronted shops with the bright lights sell new hardware.
Prices aint to good, they are struggling with economic deflation which makes the prices of certain things very low while other things so high its not worth it at all.
Depending on where you end up your better off with a guide.

My favorite computer store there was JunkWorld (.jp) but they deal with products that would be sellable to a common person, ie C2D and better - although just like my favorite-ish local computer store, if you go throughly through their website, you can find their inventory of BNC network gear and CD-Rs at full 1999 retail price 😜

Yeah, minority shops in Akihabara (= no large signs) or the usual auction/classified sites would probably be more efficient, especially considering there's a tax AND a hassle (public trash service won't touch them) on throwing away PCs, TVs, fridges, and another thing I don't remember - but for computers there are private ewaste companies that will take them free, of course for flipping or for gold...

I can't imagine normal PC stuff would be much better there.

On the other hand, it's bound to be a better place for their own native PC-88 and PC-98 equipment.

Of course, all the normal 'hot' stuff like X68000, FM Towns and the like is mostly now priced as rare and isn't cheap anywhere. NEC PC stuff doesn't appear to have got to that point yet.

You're not gonna find a lot of 90s IBM stuff in Japan. It's almost all gonna be PC-x8 with a healthy sprinkling of MSX and X68000. Very little for AT and XT.

if JPC stuff is what you're actually after (or seems interesting enough to start getting into) BEEP! is a great place to look. Huge selection of everything, both rare and common.

And what about software? LIke od BigBox PC games?

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:

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...

Cool catalogue that might interest people, no idea if it's still going

Okay, I'm back from Japan. I'm posting this in case anyone else is going and wondering where to buy retro stuff. I had a LOT of spare time; I was there for 2 months, so I visited many stores.

- Hard Off: Hard-Off barely has anything related to computers that is worth buying. Forget about Hard-Off in Akihabara; they have nothing. I was able to find two Radeon 9600s in Kichioji. Some Hard-Offs do have, however, boxed games. I saw a couple of SimCity and The Sims (in Japanese, of course).

- Akihabara (in general): Nothing but old notebooks and some peripherals.

- Nakano Broadway: There is a computer shop there, but there is nothing retro.

- BEEP Akihabara: This place is small but has a couple of retro computers (mostly Japanese 486s and stuff like that). I saw a boxed version of Windows 95 and Windows 2000. This is the only place where I was able to find boxed retro software.

I couldn't find much, but I still got a nice PS1 in mint condition and a couple of games. Things are getting pricey, though!

Maybe u can find some old fujitsu hardware