I was there for 19 days and went to Tokyo, Kyoto, Nara, Hiroshima, Osaka, and Kanazawa, so one favorite is difficult. If I had to pick just one is would Saihoji temple in Kyoto, you sit through a prayer ceremony and write out a prayer and then get to walk around the moss covered grounds. It’s super peaceful.
Expanding past that, we stumbled into the Kanazawa lantern festival where they float the lanterns down the river which is breath-taking. Library Lounge THESE in Roppongi was a great bar to hang at and wind down. And for something over the top the Robot Restaurant in Shinjuku is completely nuts - be warned this is a total tourist thing, like what some crazed person thought someone would like when thinking about zany robot anime Japanese antics.