The big ones will all be pretty similar. In addition to those mentioned so far, any Mitsukoshi store would be great. The main street in Ginza is lined with wonderful high-rise stores. Additionally, if you go to Asakusa in Tokyo, the main Asakusa train station is actually located in a basement of the large Matsuya department store. This is quite near the main Asakusa subway stops and the water taxi pier.

Since you are going to Kyoto, there is a nice Isetan department store built right into Kyoto Station that is interesting as it is actually rather narrow but very tall. It fills a corner of most of the 9 floors of the station building. Off topic for this discussion, but there is also a huge undergound shopping mall called Porta which is also attached to Kyoto Station. It might be good if you need to make some small purchases. We found a camera store for extra camera batteries and a Subway (ironically, quite near the entrance to the subway) for some picnic-bound takeout sandwiches.

I agree with Richard. If you can arrive at the main entrance of one of the big department stores just before they open, you will be made to feel a bit like royalty. My experience with this was the aforementioned Isetan store in Kyoto Station. The doors and front wall are glass. We could see the staff inside lining up and waiting for the first customers to enter. On the stroke of the opening hour, two suited and white gloved managers opened the doors with a flourish, bowed to everyone waiting and gestured us toward the sales floor and escalators. As we walked through the store, every "station" clerk bowed deeply and quietly bade us welcome. They really understand and practise customer service. My niece really fell in love with some beautiful kimonos and bolts of silk - until I translated the price from yen into dollars for her.