Although I agree about not really needing an organized tour in Tokyo or Kyoto, there have been a few 1-day tours in Kyoto that are highly recommended by folks who have used them.

For a cab tour of Kyoto, try Doi Taxi : http://www3.ocn.ne.jp/~doitaxi/index.html .

If you are walkers, Johnny Hill Walker seems to be highly regarded:
http://web.kyoto-inet.or.jp/people/h-s-love/ .