There're plenty of decent hotels in Tokyo where two people can stay for <15,000yen per night, possibly including breakfast. Look into chains like Prince Hotel and Nikko Hotel. Those are decent 3-star type accommodations. Also, if you're willing to stay in Yokohama, there are really nice hotels where sometimes you can stay for surprisingly cheap prices. I've stayed at the Pan Pacific and Intercontinental (both at least 4 stars) there for ~15,000yen per night for 2 people.