Booking hotels is Japan is not hard. Booking.com helps. And Jalan.net. And Google.
Watch out for love hotels, though. These are just among the list of innocuous Ryokans and Western hotels. Fortunately, they are usually easy to spot by their un-Japanese opulent furnishings. Sometimes, it is stated that a room is for adults only. Most reliable, however, are the reviews. A love hotel has no reviews. At a real hotel, Stephan, Juanita, and Kees leave their real-life comments.