When I last went to Japan, there were many opportunities for small souvenir (snack/cosmetic). I definitely agree with the answers written above so far! Places like the airports (especially Haneda, I have explored the entire shopping areas for Haneda and it has a ton to offer for small souvenirs food/cosmetic and you can qualify for Tax-free exempt from most of them by spending 5,000¥ and over and providing passport).
Other places like Daiso (chain of 150¥ shop), Don Quixote (also has variety of snacks, beauty products, household needs/goods/electronics) and cheaper than a lot of places; they have many locations, very common, even at Haneda airport just very small shop. I heard Tokyo station is great too since they have a lot of shops you can see. But for something all in one place, either the airport or those chain of shops! It's very easy to find cheap & good souvenirs! I got a lot of Tokyo Banana, Unagi Pie and especially KitKat from the airport.
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.