One of the most talked about fabric stores in Tokyo would have to be Tomato located in the Textile town of Nippori. If you have a couple of days in Tokyo I would definitely make this your first stop. The ground floor is stacked to the rafters with what looked like clearance fabric, priced Y100-300 a metre. There were a lot of prints that have long disappeared from the online stores. The motto here is....if you like it buy it! Chances are you won't see the print again or it will be double the price. The other thing is to come with plenty of time to spare. Most fabrics are on rolls and stacked 5-6 rolls high on the shelf. It's difficult to see straight off what there is, you have to search. Take your time, I often missed a real gem that was later pointed out to me by my sister who was trailing behind. On the upper levels you will find higher priced quilting and fashion fabrics also worth a look. The U.S. quilting fabric on the top level averaged Y880 a metre.
The sister store next door stocks buttons, trims, felt, notions, stamps and knitting needles. Worth a browse..I found a few things here. Which I noticed were cheaper than when I saw them elsewhere.
Take the Yamanote line from Shinjuku. It will take you about 20mins and the fare is Y190 one-way. Once you are out of the barriers turn right and head down the stairs. Just follow the signs to textile town.
Minimum cut 1 metre
Closed on Sunday