For snacks like kitkat, tokyo banana, you can buy at the airport. There's plenty of stores in there but I suggest that you shop after the immigration. Inside the boarding area of Narita Terminal 2, there's Fa-so-la souvenir store. They offer wide variety of Japanese goodies including Royce chocolates. What's good about shopping at the airport is that you can spend more time on sightseeing hassle free since you do not need to drag your shopping bags with you. Also, everything in the airport is tax-free. you do not need to reach a certain amount (usually 5,000yen) to get away with the 8% tax.
As for the cosmetics, prices at Kukomin, Matsumoto Kiyoshi or even Don Quijote are pretty reasonable. :)
I suggest Daiso! We had the most fun shopping in that store! Very affordable and an enjoyable experience!!
I suggest to go to Laox. As I know there are 3 big Laox in Tokyo. 1. Akihabara, 2. Ginza, 3. Shinjuku. Ohh also in Odaiba. You can find everything in this shop as you want to buy many kind of snacks, cosmetics and electro devices etc... This is also duty free shop. So please compare the price w.other shops! Here is the web site. Enjoy your shopping in Tokyo!! http://www.laox.co.jp/en/stores/akihabara/
If you are looking for "the souvenir" kind of snacks, try hitting Tokyo Station. Along the main street from Chuo Line to Tohoku Shinkansen platform, there are several souvenir shops selling snack souvenir from Tokyo such as Tokyo Banana. Yaesu shopping street, also connected to Tokyo Station, is a good idea, too.
Tokyo Solamachi, connected to Tokyo Sky Tree has a good selections of snacks, too.
For cosmetics, drug stores like Matsumoto Kiyoshi or Donki is places you want to check. For high-end Japanese cosmetics, such as red lines of Shisendo, visit department stores.