Use Japanese sites when booking hotels. Rates for the Japanese will always be cheaper. I usually use
RakutenTravel: Japan's Hotel and Ryokan reservation mega site because its in english and its easy to use.
Lots of hotels have triple rooms. Me and my friends go into Sapporo quite a bit and usually pay around 3000-4000 yen per person in nice hotels. For example the Mercure in the main entertainment district was 9000 yen for 3 king size beds.