There are many areas, where are famous for onsen (hot spring bath) in Japan and each of them have their own uniqueness in terms of the quality of onsen itself, so it is rather hard to pick the best one because there will be personal preferences for what onsen should be etc depending on each individual, but I will introduce my favorite onsen hotel in Bessho, Nagano prefecture.
Nagano prefecture is relatively close to Tokyo and you can easily visit there by Shinkansen, so I highly recommend you to visit Nagano prefecture while you are in Japan. It will take about 2 hours by Shinkansen from Ueno station in Tokyo.
Zenkoji (善光寺）in Nagano city is the most famous temple in that area (When you are in Nagano, it is certainly worth visiting there) and I used to visit there regularly because my grandma used to live in a small onsen town near Nagano city, so I have visited there every now and then. There are many other places you can visit in Nagano such as monkey onsen mountain, Matsumoto castle, Obuse chestnuts town etc, so when you are interested in visiting Nagano, please check this site.
By the way, when you are in Nagano, please try the Kamameshi bento.
Although the company is located in a different prefecture called Gunma, Kamameshi bento is very popular in Nagano, that is mainly because it has been sold in those areas on the way to Nagano, so many people purchase it when they visit there. The bento comes with the ceramic bowl and you can take it home with you (it can be used for cooking rice etc at home). It will cost you around only 1,000yen. We normally eat it on Shinkansen, so it is sold at the major stations in Nagano, but you can, of course, bring it with you to the hotel you are staying or a park for lunch.
Bessho onsen is located in the south of Nagano prefecture and it will also take only two hours from Tokyo (You have to change the trains at Ueda station to the local train to Bessho).
Bessho onsen is a small onsen town surrounded by mountains and there are several onsen hotels in that town, but my favorite hotel is Hanaya (花屋）.
The hotel was originally established in Taisho period and the buildings have been well preserved as you can see on the photo.
They have a relatively large garden inside of the hotel complex and you need to go through these corridors to go to your room and other areas of the hotel.
They have three onsen bath rooms.
There are various types of guest rooms and some of them have the private onsen bath (they normally cost more than the standard rooms). My favorite room of all is the room No.21.
Room No. 21 is the largest room available at the hotel and the room has various attractive features. The photo of the garden is from the room 21.
The photo is taken from anther room of the Room No.21. The sofa and the table of the overlooking the garden photo is located on the right hand side of the picture behind the white paper doors. This room is extremely popular, so please make sure to book the room in advance before travelling to Japan.
They are dinning rooms of the hotel (source: from Hanaya hotel HP).
Japanese hotels generally serve dinner and breakfast and the cost is all included in the room charge. They serve traditional Japanese Kaiseki style course for dinner and breakfast is a mixture of Japanese and Western style.
Unfortunately they neither have an English HP nor English speaking staff, but if you search on internet “Hanaya Hotel in Bessho”, you should be able to find the information in English. I will also be happy to give you more detail information prior to your visit, so please feel free to contact me, if you are really interested in staying there.
What I really like about this town is that it is very small and so peaceful, but there are several touristy places too, so while you are there, you can enjoy both the tranquil environment and the tourist attranctions.
I will introduce several tourist attractions of that town.
This is the main temple in that town and Kitamuki literally means facing north, so presumably it must be facing north.
Anrakuji is the oldest temple in that region. You need to go up the little mountain to reach the pagoda, it is worth visiting too.
I love sitting at the window of the temple while looking at the beautifully well maintained garden.
Nagano is famous for high quality soba noodles and you will see many soba restaurants while you are visiting there. Sobakyu (そば久） serves the best soba noodle in that town, as far as I concern, so if you feel like having soba for lunch, this is the place to go (I tried other soba restaurants in that town, but others were not worth visiting, I am afraid).
Hakone is the most popular destination for onsen for those people visiting Tokyo, because it is easily accessible from Shinjyuku and they have both mountains and onsen, but the quality of onsen is not that amusing (it will be good enough for just experiencing the atmosphere). There are also other onsen towns where are more famous compared to Bessho, but what I love about Bessho is that it is not so touristy and it has not yet been known by many foreign tourists, so you will be able to experience what real Japanese onsen like and you can also experience the tranquility of Japanese mountain area.