The biggest and most famous Japanese travel agency. If you want to reserve a hotel just use Rakuten Travel. Great place with great support in many Languages! But there is no Language switcher for mobile. You will need to change to PC mode. The mode change button is in the bottom part of the website.
Rakuten Stay is very similar to airbnb. You can reserve Private accommodations and simple lodging from this sites. So cheaper compare to Hotels. If you want to reserve Hotel in Japan, use rakuten Travel and if you want to Reserve airbnb use Rakuten stay.
Japan Travel Agency is the biggest Japan-only travel company in Japan. So that to reserve a hotel in Japan this website is also really great. The problem is there is English as well but can not reserve it. If you want to reserve you will need to use Japanese.
One of the best part of TripAdvisor is its extensive collection of user-generated reviews. Travelers can share their experiences, insights, and tips, helping others make informed decisions about accommodations, restaurants, and attractions. You can find not only hotels but also other good place to go around hotels!
HIS is also a super popular website for Japanese to reserve Hotels in Japan. They do have English as well but little wired because of auto translations. However, they do anime collaborations frequently, which I recommend as Otaku! Now they doing Frieren.