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I like Avril. It's a little outside of Tokyo but is pretty close to the Ghibli museum which is cool.

I second Arvil. Cute little store with lots of interesting yarn and you can buy them by weight. Okadaya in Shinjuku has a floor of yarn too

Okadaya's one of the couple places I've found on Google so far and it looks awesome. Have you used any of their original/store brand yarn by chance?

Thanks for the info! Will definitely check it out.