http://www.japaneseguesthouses.com/index.htm
In Kyoto you absolutely must see Kiyomizudera. It's a temple built into the side of a mountain with an amaing view over Kyoto. That area is particularly beautiful in the Spring, so lucky you.
As long as you're in Kyoto you should check out Osaka and Kobe too. Osaka is right next to Kyoto and is the coolest fucking city on the planet. Great food, great culture, great music. Amemura (America Town) and the area surrounding Namba station is a complete neon light pachinko bar clatter jpop mindfuck. Your Japan experience isn't complete without it. There are also alot of cool record stores in that area (alchemy records - time bomb records).
Kobe can be pretty cool too (I used to live there!). There is a bizarre shopping district underneath the train linese between Motomachi and Kobe stations filled with all the outdated electronic bullshit you never needed. This is where you buy your pornographic videogames, Nintendo prototypes, ancient computers and vintage music gear. A must see.