There are several flea market in Tokyo selling pretty much everything, many for refurbish clothing and shoes. But if you're looking for some Japanese old stuff and some antic my two best picks are Monzen Nakacho flea market and Yasukuni shrine flea market. The latter is my top favorite.
It's every Sunday morning in the side alley going to the shrine. The number of people depends highly on the weather, and it might not take place during the special festival of the shrine. Every time I go I find something!!
A few years ago I found this beautiful iron lion head that I've offered to my sister for her Parisian-Japanese interior.