Good question. When I visited Tokyo I was impressed by the large number of guitars and there are many ukulele players and enthusiasts in Japan. Hawaiian uke stores make good money from Japanese tourists who buy their ukes there. If you search for very specific ukes on EBay often Japanese sellers/stores pop up and their inventory can be extensive. I was looking for a specific KoAloha and the only ones available were from Japan. But shipping and customs added a lot to the already high price. But Ebay is definitely still a good place to find ukes sold by Japanese stores.
In my experience, prices in Japanese stores are great for Japanese brands, but high for imported brands because of the high importing costs. If you're looking for an American-brand ukulele, you can find much better prices in American stores.
Two stores that I liked in Tokyo are Kiwaya and Ukulele Mania. If your English is better than your Japanese, Ukulele Mania is a good choice since the manager is American-born and speaks better English than Japanese. These stores sell a lot of great Japanese-brand ukuleles that are hard to find in the USA. I believe they have some kind of tax rebate program so that foreigners (with foreign passports) don't have to pay local sales taxes.