In 2026, I stayed right next to 品川駅, which was really nice, since you have direct connections from both 羽田 and 成田 and to the 新幹線 to 京都. The same holds for 上野 (bearing in mind that the train to 成田 leaves from the Keisei Ueno Station rather than the JR station).
The Nezu museum and the much smaller Hatakeyama museums are always worth checking for special events.
京都
There are 月茶 on the 1st and 15th at Kitano.
Absolutely book lunch at the famous 一休 and breakfast at 瓢亭
長岡京
About 20' south of 京都, famous for it's bamboo. 利休's 体安 is here (reservation required). Here you also have the impressive 天満宮 shrine.