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.
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.
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.