There are a number of regularly-held flea markets throughout the year in Tokyo. Listings for a number of flea markets, including specific event schedules, can be found here: http://www.paperlantern.net/fleamarket/.
Some frequently-held flea markets include:
Best Flea Market, Held every second Sunday (weather-permitting) from 10 a.m. to 4 p.m. at the Tokyo International Forum, 3-5-1 Marunouchi, Chiyoda-ku, Tokyo, regularly boasting around 250 dealers selling a variety of wares. For more information, contact the NPO OMY Area Management Association at Tel: 03-3287-5386.
Oedo Antique Fair, Held on the first and third Sunday of every month (weather-permitting) from 9 a.m. to 4 p.m. at Tokyo International Forum, 3-5-1 Marunouchi, Chiyoda-ku, Tokyo, is popular with both Japanese and expat audiences. The more than 250 vendors sell artwork reflecting Japanese history, ceramics, kimonos, and other Japan-related articles. For more information, visit the organizer’s Web site at http://www.antique-market.jp.
Shinagawa Intercity Flea Market, Held rain or shine every Sunday (except Jan. 1, and the third Sunday in Feb. and August) from 10 a.m. to 4 p.m. at Shinagawa Intercity, 2-15-2 Konan, Minato-ku, Tokyo, with 120 vendors selling a variety of wares.