If you've got hotel/air packages available to you where you live, look into their pricing to see if they're cheaper.
If you're booking both hotel and air on your own, there are cheap non-capsule places that work more like hostels in other countries, like these.
And if you've got the budget for it, I'd suggest you go one class higher for hotel. Stay at a "business hotel" such as Toyoko Inn. You get a room and ensuite bathroom to yourself.
My preferred locations for Tokyo are the smaller stations on Yamanote line, a stop or two away from a major station, less hustle & bustle. Example
http://www.toyoko-inn.com/e_hotel/00139/index.html (Otsuka, a stop away from Ikebukuro, you can walk if you have 10-15 mins)
http://www.toyoko-inn.com/e_hotel/00135/index.html (Uguisudani, a stop away from Ueno)
In any case I think the hotel options in Tokyo are much better than Hong Kong.