Harmony House is great. It's in a wonderful location close to many train lines and incredibly walkable. It is small, and you do have to walk up four flights of stairs, so not for over two people, or people who struggle with stairs. My husband is 6'2 and while a little tall for the ceiling, he still enjoyed the experience!
The room is beautifully & traditionally designed. There were soaps, and even toothbrushes. Tea, coffee, and a water pot are there for morning refreshment.
Daisuke is an amazing host with fantastic recommendations, especially for those interested in history and architecture. His food recommendations were excellent as well.
The bar below and Min Min are awesome. Try the Hoshiko! We didn't hear much noise from there, but if you are sensitive they do provide earplugs.
There is also a bakery just below with sweet treats and good coffee. The area has a ton of food. You could eat at a different place every night for weeks and still not try everything.
15C is a great place for breakfast. The large sit-down one, not the small bakery only.
Overall a fantastic place and area. We loved our trip here!