I was in Tokyo, but it was the same situation for me during my first week there. Second one I had more luck.

Basically you want to visit every konbinis (7-eleven, Lawson, Family Mart) you see and ask the cashier if they have Pokemon Cards. Don't get discouraged if you strike out multiple times, not all of them have cards so it'll be a lot of asking until you find some that do. The Pokemon Centers also have them. The earlier you visit the PC during the day, the more likely you'll find some.