I know we frown at link only answers but here is the same question with many answers on Reddit. I have copy-pasted the relevant excerpts below.
there's a budo shop down the street from the kodokan that sells
kusakura judogi as well as their own brand. the kodokan store also
i have bought from the shop down the road and they are fine, but as a
foreigner i suggest contacting the owner of budo
export who is very helpful and can get
and mitsuboshi judogi in adition to his own
all the brands have "club" models that are a lot cheaper.
he can ship within japan and he also let me meet him and pick mine up
in person. great guy. he is french but his english and japanese are
very very good. use google translate on the website if you need to.
don't go to the seido english site as that's only aikido stuff.
I bought a kuSakura pants from the shop down the road from the
Kodokan, they were very friendly. They also sell some cool cloth with
kanji it for decorating the dojo. I liked the Kodokan shop on the 1st
floor though, they probably have everything he needs :)
There's Sakuraya near Kodanshita Station
Definitely check out Iwata Shokai as well.
http://iwataco.com/frame2e.html They were one of the earliest
suppliers to the Kodokan, which they are very near, and though their
dōgi are labelled aikidogi, they're actually judogi. (I am fairly
certain that the house brand dōgi sold by Budo Export and Tozando are
actually rebranded Iwata ones.)
I went to the Isami store in Suidobashi (for a BJJ gi). They have a
few different brands and if I remember they had a sister store down
the street with even more options. Not sure on price though, the
Isami I bought was right around 30000 yen (but I think Isami is known
as a higher-end gi). http://suidobashi-isami.com/ (BJJ, not judo)