Denim/Americana/Workwear: Hinoya & Americaya in Ueno. Is Base Control still a thing? That has a Uniqlo vibe to it, as far as basics go.
Other than that, just stick to Shibuya (Harajuku/Omotesando area) for the majority of shops.
Personally, I am a huge fan of the resell/consignment/second hand shops in Japan, namely Kindal and Rag Tag (Jumble Store, to a lesser extent). Both have a good number of locations in Tokyo.