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Japan has an incredible range of options when it comes to accommodation: from Western-style hotels with the most luxurious rooms, to modern, futuristic buildings, passing by young and artsy hostels or minimalistic staff-free condos. But what you should try at least once going to Japan is the Japanese-style accommodation like ryokan or minshuku, which could likely be one of the highlights of your trip! Here is a list of different types of places where we stayed and that we all found on Booking.com.
You can find Western-style hotels in all big cities, including all major chains, with a large choice of places. Rooms are usually small and sometimes even divided in two sides to optimize the space if you just want to occupy two beds, but in general they are modern and full of little amenities like pijamas, slippers and toothbrushes. Most hotels have free wifi and both continental or Japanese breakfasts and normally they would have somebody who can speak English.
Other Western-style accommodation are hostels and guesthouses, that are much more abundant in Japan than you may think - some of them really looking more like modern hotels than the crappy places you have in mind! We stayed in a couple that really surprised us in terms of organization, cleanness and services, so I really recommend them, especially if you are only in that place for one night and you need an easy and convenient place to stay. The girls particularly enjoyed the atmosphere in some of them, and loved to hang out in the communal areas where you usually meet all kinds of travelers.
There are other very Japanese ways of spending the night, like capsules hotels or love hotels that we haven't tried any of those.
There is an incredible offer of Japanese-style hotels, which are roughly divided between the (sometimes) more fancy ryokans and the cheaper minshuku. Ryokans are usually in old historic houses (some of them even in villas surrounded by beautiful parks) and what you book is usually a furnished room with a low table and floor futons sitting on tatami, surrounded by decorated paper walls and Japanese art. Sleeping on the floor is much more comfortable than you might think and staying in places like that, which usually also have a communal bath (sento) and a small garden for sure will allow you to have an incredible cultural experience! Some ryokans are simple and quite, some others are big and luxurious and in general they are never cheap, given that you also pay for service that you sometimes have (in some places they roll out the futons ready for you, usually when you are out for dinner). We got a good deal a couple of times in reserving at the last minute, or going off-season to onsen areas where ryokans offer a half-board pension with the access to the fantastic bath and two amazing meals included!
Minshukus are family-run guesthouses that generally have only one or two rooms and are cheaper and simpler but definitely an interesting experience and sometimes the only option in more rural areas. Unfortunately we didn't get to stay in one of those but I heard it's an interesting experience.