Booking stay in Tokyo from local websites

So, I have lived in Tokyo for 3 years a while ago, and I am returning for a holiday early next year. I am now realizing that I have no clue how to book a stay if not with Western websites (booking.com etc..), which I’d guess it’s not the best way. Any Japanese website or any other tool to get better options? I speak and read Japanese.
I only see Western hotels on the websites I’m looking at now, but I wouldn’t mind a 旅館 too.

6 comments
  1. – Yahoo Travel (usually good discount thanks to ポイント即時割引 system)
    – Rakuten Travel
    – Jalan
    – travel agencies like JTB

  2. I find booking gives the best prices, but if you go directly to hotel websites they sometimes have nice package deals

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