As promised, let me introduce you to my favorite yarn shop in the Tokyo metropolitan area, Avril.
Avril sells Habu yarn. You should have a look at the Habu Textiles website for more information about the different fibers they sell. Be careful not to stay there too long ;)
Avril is located in Kichijoji, at the end of the Keio Inokashira line which you catch from Shibuya. I am lucky enough to live close to the shop; it takes me 20 minutes from door to door! So this little yarn haven has a very interesting business model: they sell yarn by weight, with 10g as the minimum purchase. All of the walls in Avril are covered with huge spools of yarn. The labels tell you how many meters are equivalent to 10g of each type of yarn. Once you've selected your fiber, a shop assistant will reel your yarn on a spool.
If you find a great fiber but not in your desired color, you can always buy natural yarn and dye it at home. More interestingly, the shop's staff can help you create your own yarn by combining different fibers together.
When I returned to Avril last week to buy more yarn for my future jumper, they recognized me and we talked as if we had known each other for ages. If you are interested in buying some yarn from Avril, they do support English-speaking customers and ship internationally. Have a look at their online catalogue and order by email. Avril sells yarn sample catalogues for each type of fiber as well for only 150 yen (approx. $1.80). I am praising this shop so much because, in knitting as in sewing, a great result depends on the quality of the material.