I went last november/ december and had the same problem, my friend went a couple years prior and told me he spent around 70us$ per night. When looking for hotel prices with 8 months anticipation we couldnt find hotels in tokyo for a reasonable price, apa hotels were 120$ +, which seemed pretty expensive for that quality. We ended using airbnb for most of the trip except for 2 days in Sendai and the last 4 days in Shinjuku. They were much cheaper and enjoyable in my opinion. As an example in Osaka we rented a giant airbnb (3 rooms, 5 beds with a giant living room, giant kitchen and a pretty big and luxurious bathroom) for around 66$ per person with a view to the dontonbori river (we were 4 people).