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!
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/