I'm currently in Japan, and want to buy Apple products as well. You can get pretty much every Apple product at larger electronic stores that also do Tax Free. When it comes to MacBooks there's always the issue with non-Japanese keyboards. They usually don't have many US-keyboard MacBooks in stock, if at all.
They offered me to order it with a US-keyboard, but then it wouldn't be tax-free anymore, as they ship it directly to your address in Japan. Therefore, you can go to an Apple Store, where they often have US-keyboard models in stock, but also don't do tax-free.
Best chances to find an electronic store with US-keyboards in stock is definitely Tokyo, haven't been lucky in Kyoto and Osaka so far.
Even without tax-free MacBooks for instance, are still 20% cheaper compared to Europe, for example.
Hope that helps :)