There are many different types of hotels and accommodations in Japan to suit any tourist. I would highly recommend that every visitor to Japan experience some of the bathing culture that has been predominant here for hundreds of years, due to the naturally occurring hot springs (onsens) in most regions. There are many types of accommodations through which you can enjoy hot springs during your stay. Three main types of accommodations are minshuku, ryokan and onsen hotels. These accommodations are of varying prices and standards, but most will offer the facilities of hot springs or public bathing as part of your stay. For Japanese people, a good bath is an absolute necessity when traveling.
Onsen 温泉（おんせん）can be described as the source of natural hot springs, or the water that has been derived from that source. Natural hot springs can be divided into two kinds: those that are created from volcanic magma, and those that are created through other sources. Not all accommodations will offer natural hot spring facilities, but there are generally always public bathing facilities, unless staying in a western style hotel.
The most basic kind of onsen accommodation is minshuku. Minshukus民宿（みんしゅく）are mainly run on a relatively small scale, by a family or as a secondary income, for example. They typically have Japanese style rooms with tatami flooring and futons for sleeping. Amenities tend to be basic and the prices very reasonable. Minshukus can often be found in smaller fishing and farming villages, and often include a pretty good breakfast and dinner included in the price of the stay. This kind of accommodation can be a little harder to book on the internet, but can be found in most areas of Japan.
Ryokan旅館（りょかん）is the most well known, traditional style of Japanese accommodation. The architecture is of a traditional style with accompanying décor and interior. Of course this includes tatami flooring and futons for sleeping. Ryokan accommodations often offer the option of having your meal served in your own room. An array of beautifully prepared dishes will be brought to your room at the time you decide, and a hostess may explain each dish, how it was prepared and how you should eat it. Onsen hotels are more of a fusion of modern and old, with the option of western or Japanese style rooms, restaurant dining and a variety of other amenities.
For a first time visitor to Japan, an onsen hotel, with larger scale facilities and the possibility of English speaking staff may be a nice way to ease into your stay in Japan. However, staying in a ryokan or minshuku would also provide a different insight into Japanese recreation and how most Japanese people like to spend their vacation time. Even with very basic amenities, minshukus often have very delicious meals included in the price, and the service in a Japanese ryokan is second to none.
There are many good internet sites to search for different kinds of accommodations in Japan. Rakuten travel or Japanican are good examples of sites that will help you find the accommodation you are looking for. When enjoying accommodations with public bathing facilities, be sure to make the best use of the facilities, trying all the baths and going more than once a day if you enjoy it. Japanese people often go to these accommodations without any real plans except to relax and enjoy the hot springs three to four times in one day. It can be an extremely relaxing way to enjoy Japan. A day of bathing in the hot springs followed by a sumptuous meal brought to your room makes sleeping on a futon even more comfortable!
When using the bathing facilities, be sure to observe the bathing rules and if you are not sure, follow what others around you are doing. For more information, look here or here. Whichever place you decide on, I hope you enjoy your stay!