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.
All the above answers are GREAT!
Especially, if you want to buy in volume, yes, the Airport will be the best choice...
I also happened to find Shinjuku Takashimaya Duty Free Shop where they carried (at that time) various KitKat (once I found Sake Flavor one!) aside from other souvenir snacks.
I can't say if the prices would be cheaper though. Please make sure to read: https://www.takashimaya-dfs.com/en/guide/index.html
If you want to get cheap souvenirs, (as previous people mentioned), your choice would be Daiso (equivalent to Dollar Store in the US, but MUCH BETTER Quality!), Don Quixote (you can find whole bunch of array of STAFF!)... However, sometimes you may find some unusual & interesting things at various convenience stores as well...
If you KNOW specific item you want, I agree/recommend to order through Rakuten Global.
If you have a Japanese friend who has Amazon Japan Prime membership, maybe you can order thru them as well.
Good luck and Have Fun Shopping in Japan!
I recommend don quixote, they have a great selection.
I think you can just simply order from Rakuten Global Market as I did:
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.