How small a group is “small?” And what kind of experience are you looking for—-an overview visiting a number of cities, staying in Western hotels, or a slower, more cultural-focused pace, staying in small inns and ryokans as well as Western-style hotels?
I ask because we really liked the adventure travel company MT Sobek for our first trip to Japan (2019). The trip includes some moderate hiking, on the historic Nakasendo Trail, as well as time in Kyoto and Tokyo. Also historic Nara, and the Buddhist temple complex of Koya-san (Mt. Koya), where we spent the night in temple lodgings. In Tokyo and Kyoto, we stayed in very nice Western-styl hotels, but for the rest we staying in charming mountain inns and ryokan, in lovely tatami rooms with futons for bedding. Nice onsen soaking areas, separate for men and women. The meals were amazing—-a beautiful array of small dishes at breakfast and dinner. Our group totaled 7 people, plus our guide Ryoko-san, who gave us wonderful little lectures on Japanese history, religion, art, and more.
https://www.mtsobek.com/trips/asia/japan/japan-kyoto-to-tokyo-walking/
I would highly recommend a trip like this if you truly want to experience the beauty, comfort, and cultural riches of Japan.
We enjoyed that trip so much that even though we felt capable of traveling independently in Japan, we shoe another MT Sobek trip (the Kumano Kodo) for our trip last November. This one too was wonderful, with 10 people and 2 guides. The hiking was more difficult that the Nakasendo trip, and I would not recommend it for a first trip to Japan.