don't know about Tokyo but if you don't stay in a japanese inn in Kyoto, do try the GrandVia hotel, located just above the amazing Kyoto station. In Europe, station hotels have a very bad reputation as a nest for crime and prostitution, in addition to noise, but in Kyoto, the Granbvia is a luxury place, silent and very well located. you can get a beautiful room for as low as Y 14,000. Don't take your breakfast at the hotel ( about US$ 25 for a so-called buffet), do instead try the nice italian cafe located in the basement of the station, which is very cheap for Japanese standards and offers good coffee and a wide range of pastries, croissants etc.