I'm specifically looking for some linocutting tools (speedball nibs, inks etc). Amazon has bizarrely inflated prices, I presume due to importing (¥10,000 for a box of nibs worth about £10). So, where's good?

Curious to see if anyone has better suggestions but there are some tools, inks and papers in Sekaido (I saw them in the Shinjuku store, not sure about the one in Yokohama). However their selection is a bit limited so when I was looking for an etching needle I bought it online on this website: https://www.zowhow.com/c/printing

I'm not sure if Tokyu Hands would have exactly what you are looking for, but I find this particular store in Shinjuku to be better than most of their shops. You might have luck there.
https://goo.gl/maps/EhNZZ78HZh6wRrZM6

I go to Bunkado in Jimbocho. I do the equivalent of linocuts with the blue/green rubber material they sell here, and this is the best place I've found so far.

They don't seem to have a website but here's the address:
〒101-0051 Tokyo, Chiyoda City, Kanda Jinbocho, 2 Chome−２４−10
(if you just google 文化堂 神保町 it';; come up).
It's a three storey art supply store and one floor (admittedly small) is dedicated to relief printing, etching etc.

Thanks all for your replies! Appreciated. Keen to go into a store, but good to know about zowhow (although hard to look at 😂)
Ben - this sounds perfect.