There are a few big fabric and craft stores located in Shinjuku.
Open daily from 10:00-20:30
Okadaya is near the East Exit of Shinjuku Station. It's a store with 6 floors, that has fabric and sewing supplies. From Okadaya it's about a 15 minute walk to the Takashimaya Building on the South-East side of Shinjuku Station. In here you will find two more craft stores:
Open from 10:00-20:00
This fabric shop is on the 11th floor of Takashimaya. Minimum cut for fabrics is usually 10cm.
Open from 10:00-21:00
TOKYU HANDS deals with all kinds of products, such as high-quality and high-functional livingware, fancy made-in-Japan bags, convenient travel goods, the latest Japanese stationery, unique articles, topical beauty products, and tools and materials for DIY.
It's located on the 2nd to 8th floor of Takashimaya.