Large parks in Tokyo
Many large parks in Tokyo such as Shinjuku Central Park, Yoyogi Park, Komazawa Olympic Park have regular flea markets throughout the year.
However on the other hand there are many who enjoy flea markets, and see it as an opportunity to do some unique shopping, as opposed to just going the cheap route. I personally only shop flea markets for the price, but in Japan it's a very nice family outing, even for those who might claim to be a "new" kind of person.
The schedule is here for some of these parks. It's in Japanese, but this page could easily be printed out and explained by a Japanese person, if you're interested in doing some flea market shopping during your time in Tokyo.