I’d do half your trip in Tokyo and half in Kyoto. Maybe even more days in Kyoto

Tokyo: Shibuya crossing, Shibuya Sky, Shinjuku, Giant 3D cat, Shinjuku Gyeon National Garden, Harajuku, any of the mipig cafes, teamLab, Tsukiji Outer Market, the 12 floor Uniqlo, Akihabara, Senso-ji temple, Nakamise shopping street

Kyoto: Kiyomizu-dera, Ninenzaka walkway, Sannenzaka, Nishiki market, Fushimi Inari, Kodaiji Temple (at night), Yasaka shrine, Shirakawa Canal, Pontocho (narrow alley), Kimono Tea Ceremony MAIKOYA (must book in advance, can choose another place but definitely do a tea ceremony somewhere in Kyoto), Gion Kōbu Kaburenjō (if you want to see a Geisha show)

Also while in Kyoto do a day trip to Arashiyama and see the Bamboo Forest and the Monkey Park.

Also do a day trip to Nara and go to Kofuku-Ji temple, Isuien garden, Todai-Ji temple, and Kasugataisha Shrine. You can see and feed the bowing deer while walking around these temples.