If you are travelling to Tokyo but find it difficult to book budget hotels, try vicinity areas where accommodation tend to be cheaper. Yokohama would be the one, as there are range of budget hotels and good public transport network to/from Tokyo (30-40min by JR, Keikyu Railways and Tokyu Railways).
Where to find budget hotels in Yokohama?
Kannai Station ( JR ): Quite many budget hotels are found around the station including popular chain hotels e.g. APA Hotel, Toyoko-Inn, Super Hotel. Plenty of eating outlets, easy to get around Yokohama but the area itself is not very much touristic.
Sakuragi-cho Station ( JR ): More budget hotels are located on the west side (downtown area) of the station, while several chain hotels e.g. Washington Hotel, Toyoko-Inn, are located on the east side (bay area) stretching from Minato Mirai 21 (MM21), Aka-Renga Warehouse, all the way to Yamashita Park.
Yokohama Station ( JR / Keikyu / Tokyu ): It is the terminal station in the city, convenient to get around either to Tokyo or Kamakura direction.