There are quite a few good ones in kyoto, Arashiyama has an ok garden in the temple area the bamboo forest is there too, there are a few nice restaurants that have good gardens can t think of the name at the moment but can look it up if you like, you may have trouble finding it depending on your japanese but the one im thinking of has a great 6 or 7 coarse meal degestation type stuff but japanese food of coarse. If you go to Himeji castle in Hyogo there is a really good garden next door, slightly to the south, its famous for something but I cant remember. Himeji is well worth a visit and will probably take 1.5-2 hours from JR Kyoto station, on the Kobe Line, stop in Kobe too! go to the earthquake (Hanshin-daishin) memorial exhibition.