Ginza Akebono is a must-visit wagashi (Japanese sweets) shop in Tokyo. They have many branches around Tokyo and there is sometimes a line-up. But after trying it, you will understand why. They have seasonal sweets too, such as sakura. One piece is around ¥273.
Toraya is a high-end wagashi store and their store is aesthetically great! They have seasonal sweets and desserts and is definitely worth stopping at. Or it makes for a great souvenir for someone you love. This store was founded in 1526, so I guess it's safe to say it's been around for a while! They have shops all around Japan, and 6 in Tokyo. Have you tried the azuki and chocolate fondant?
Takemura is in its original 1930 building, which is considered to be a Historical building. Tucked away in a small and interesting neighbourhood near Ochanomizu, this shop is a little hard to find. But, it's worth the trouble. You should try their sakura water and their deep friend Manju.
1-9 Kanda-Sudacho, Chiyoda-ku Tokyo
Oosumi Tamaya is famous for creating the original "ichigo daifuku" (strawberry covered mochi) and the original store is in Shinjuku.
Ichigo daifuku is a delicious dessert because it is soft and has an interesting texture, and the taste has the right balance of sweetness. It is a Japanese classic that you need to try! A piece is ¥230.
8-25 Sumiyoshimachi, Shinjuku, Tokyo
Nagato is a 300 year old Japanese sweets confectioner located in Nihombashi. They have loads of seasonal sweets to try from, such as yuzu. It is definitely worth trying. It is ¥350.
3-1-3 Nihonbashi, Chuo-ku, Tokyo