Rakuten Travel is the biggest and most famous Japanese travel agency. If you want to reserve a hotel you can just use Rakuten Travel which is a great place with great support in many languages! The auto-translate feature is limited to PC only. You can switch to PC mode using the button at 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.
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Japan Travel Agency is the biggest Japan-only travel company in Japan. This website is really great for reserving hotels in Japan. A problem you may encounter is that you can only reserve a hotel in the Japanese version of the website.
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One of the best parts 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 more than just hotels, but also nearby attractions!
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HIS is also a super popular website in Japan to reserve hotels. They do have limited English auto-translations. However, they do anime collaborations frequently, which I recommend to Otaku! Right now they are featuring Frieren Beyond Journey's End.
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From Soft Bank
From Docomo
↑(Click img above for hotel reservations)
This is the biggest and the most popular travel company in Japan!! You can reserve hotel at reasonable price!! There are English, Thai, Korean and Chinese version for Rakuten!! You can switch it from language. If you're using Smartphone, change website to PC version and switch the language to your language.
To stay in Japan, Japanese site is always the cheapest.