There are lots of flea markets in Tokyo but most of them are held irregularly. This is one of the website that gathers flea market information in Tokyo: http://furima.fmfm.jp/?area_id=104&pref_id=13 (Japanese Only)
I think the flea market in Yoyogi Park (Harajuku) is the biggest and most famous. It's held about once in a month. This Facebook page has information about events in Yoyogi Park: https://www.facebook.com/yoyogipark.info/
If you are visiting Japan in May, you can visit the flea market that called "Tokyo-nominoichi". It will be held on May 13th and 14th. This flea market is really amazing and you can find the one that really satisfies you!