I guess it might be Harajuku, especially in Takeshita Street. Those are mainly for teenage girls, but sometimes have clothes follow the trend from some hundred yen.
Or hit Shibuya and visit fast fashion stores; H&M, Forever21, ZARA, Uniqlo, GAP, etc. Shimamura is another great place to find cheap clothes but most of the branches are not in downtown. The only store near downtown is located in Takadanobaba, which is two stops away from Shinjuku Station by train.
Ameyoko Street in Ueno might have cheap items as well, since Ueno (and Okachimachi) used to be a wholesale district.