Japan is one of the most beautiful places in the world. Most important travel advice: set out each day with only one thing planned or you could totally overwhelm yourself with logistics. Countless friends said Tokyo was their favorite place to visit because there was something crazy to see at every turn. I agree that Tokyo is a very "alive" city and it will keep you entertained but without any hesitation, Kyoto is my preferred city because of the incredible history, art and natural landscape. And the snow monkeys, those guys are rad!
Where to Stay in Japan
In Tokyo I recommend the Hotel Villa Fontaine and in Kyoto the Almont Hotel. For traditional Japanese accommodations I found the best Ryokan collection in the country. Whichever you choose, book with Agoda who typically have the best rates in Asia.