Nipon Ukulele Association: NUA was established in 1959 by Mr. Harry Haruko Haida expressly for amateur players. Located in Kawasaki, just a 15-20 minute train ride from Tokyo Station, NUA holds meetings on the 3rd Sunday of each month. Check their website for more information!
T's Ukuleles: Hand-built and custom-built ukuleles designed by master luthier Shinji Takahashi
Rolling Coconuts is a Japanese ukulele magazine published quarterly. RC makes back issues available in an online version but the text is strictly in Japanese and you need to go through a 3rd party provider. If you go here you can see a few pages of select issues by clicking on the blue button marked ちら見. If you're tempted to read more, you can pay ¥400 (about $4) to download the full magazine but registration is something of a bother if you don't read Japanese. Either way, it's fun to see what topics are of interest to Japanese uke players!
Coustii: You can find lots of good information and how-to articles and videos on this site. Give it a look!