Flea Market in Yoyogi Park must be the most famous one. There are hundreds of people participate in as well as customers. Also the flea market in Yoyogi Park is more concentrated to younger generations.
If you are looking for antique goods, Oedo Kottoichi is the largest in Tokyo. The place is Yurakucho, near Ginza and conducted almost once in a month.
Tokyo Nominoichi offers a lot of fun, too. It's only once in a year.