If you're more keen on value rather than a central location then try the Shinagawa Prince, it's at Shinagawa, strangely enough. Like most Japanese hotels it's rate vary according to the size of the room but they are considerably less than comparable ones in the city centre. That said the hotel is directly opposite the enormous Shinagawa Yamamote and Shinkansen Station so you're at Tokyo Station in ten minutes door to door. If you're in the executive tower you've a great view of the trains leaving and arriving and if you look to the left you've the classic Tokyo skyline. I stayed there last year and it was a great, low cost base to explore the city from. Also if you're not too keen on the missus, many japanese hotels will do you two single rooms for less than the price of a double!!