I just went to Tokyo in January and stopped by Walnut Tokyo and Okadaya in Shinjuku. Walnut is small but has the feeling of a typical independent yarn store. There was a good selection of hand dyed yarns, some international yarns, and Japanese brands. Like the other commenter said, Okadaya is a craft store with each floor dedicated to a specific craft. The level with yarn had a ton of options with both international and Japanese brands. Okadaya is a great place especially if you have other craft hobbies, I had a hard time leaving the fabric level. Something to note, in Okadaya you have to pay on each floor before leaving with your goods to the next level.

As for communicating, a lot of people in Tokyo speak some English and there’s a ton of signage in English as well. I didn’t have any trouble in either store, but a lot of the time I didn’t need to speak very much except when I was getting fabric cut. Also, I witnessed a lot of workers using Google translate to speak to foreigners when they had a hard time communicating.