Nyanpasu~!
If you want to find Comic Yuri-hime nearby Kyoto Station, I recommend "Õgaki Syoten Kyoto Yodobashi ten" and "Animate Avanti-Kyoto".
If you don't care the distance, you SHOULD go to "Animate Kyoto". Also there are many anime-shops (such as Gamers, Toranoana, Melon-books, Lashinbang)...