I am a local and I often go to Shinjuku, Shibuya, and Yurakucho to shop for clothes, bag, shoes, and cosmetics. Specific department stores would be LUMINE, Seibu, Mitsukoshi, Marui, etc. When I was a teenager, I used to visit Harajuku every weekend. I loved walking around Takeshita Street and Ura-Harajuku.
I have visited Kappabashi to buy some kitchen utensils but it's not an everyday place to go. I was looking for specific frying pan.
I would say that the Shibuya is the place for the clothes (for young generation). And Ginza Mitsukoshi is for the groceries. Kinokuniya for the books and Akihabara is for the electrical appliances.
I would recommend to targeting what you need, and then find the best place where the locals shop.