Matilda - We’re in Tokyo right now, though we go most years as I have family there, so less of a holiday. Currently doing lots of teenage girl shopping, which is hard work. It’s hot but bearable as there is a little cloud, but make sure you’re ready for the heat if you go in July / August…
I’d say it depends a lot on what sort of things you want to do, but a few suggestions below:
Tokyo - 4 nights - see the imperial palace, Asakusa, fish market, and a day shopping such as Harajuku etc. Buy some good Japanese knives in Kappabashi St near Ueno.
Kyoto - 2 nights - kyomizu dera, and a day just wandering around and taking the atmosphere.
Nara - 1 night - go to todaiji and the deer park, but be prepared to get nibbled.
Go to a hot spring resort for a night. I’d suggest Kusatsu or Ikaho in gunma as they’re relatively accessible from Tokyo, and Kusatsu in particular is quite unique.