I would try the Hanazono Shrine Antique Market in Shinjuku. In addition to kimonos they offer used books, hanging scroll art, prints, and accessories. Like anything secondhand it can be hit-or miss on what is available when you are there.
Alternatively if you are willing to travel a bit (4.5 hours) the Kimono Flea Market Ichiroya is one of the best places to buy a genuine secondhand kimono in Japan. To get an idea of what to expect they have a really good eBay store that you can browse.
Hanazono Shrine Antique Market Schedule Every Sun (Closed on Shrine activity days and rainy days) Open hours: Sunrise - sunset Address: Hanazono-jinja shrine grounds, 5-17-3 Shinjuku Shinjuku-ku
Thrift store called Chicago, they have a large selection of kimono and yukata; I went to the one in Kyoto 3 years ago and bought 3 beautiful pieces at reasonable price :) In Tokyo go the the CHICAGO – Omotesando. More info: http://jennysretro.com/vintage-shopping-guides/retro-guide/
Yukatas are reasonably inexpensive. I bought one first-hand off-the-rack at an ordinary clothing store in Izu Inatori just before a festival. I can't remember exactly how much mine was, but it was comparable with the cost of an ordinary piece of western-style clothing. You don't need to buy one second-hand for cost reasons unless you're really watching the pennies.
(If you want to see it, go to slides 55 and 56 of Travel Night: Japan)
Wikivoyage's guide to Purchasing a kimono (which covers other Japanese clothing than actual kimonos) says that there isn't much of a second-hand market for yukatas:
Yukata make good souvenirs and gifts because they are more practical and easier to wear than kimono. However, people tend to hang onto these precisely for that reason, and therefore there's less of a second hand market.