How long will you be in Kyoto for? When I went, I really wished I could have stayed longer than I did, because there's cool stuff EVERYWHERE. I went to the Kyoto Handicrafts Center (which may not be the *actual* name, but I can look at the brochures and stuff that I saved) - it had at least five floors, lots of shopping, areas where people demonstrated traditional crafts, and the top floor had hands-on activities. It was also nice because most of the staff were English-speaking.
Other stuff you should do in Kyoto: go to Gion (the main 'upper crust' shopping area, and also where the Kabuki theatre is and where Geisha can be spotted; it's very pretty at night because of all the old-style lamps and such), then, a few streets across the river from Gion is a huge fish market, but the streets in-between are awesome for cheaper shopping. I found some thrift stores there and I think the staff started to recognize me because I kept going back to them and finding more stuff.
And, of course, there are a lot of temples and shrines you won't want to miss. Will you be going to Fushimi-inari or Himeji Castle?