Are there local micro-breweries in Tokyo?
Are they serving local Japanese craft beer?
What are Japanese craft beer that one can find in Tokyo?
You can find a lot of different bars that sell micro-brews in Tokyo.
most All of the micro-breweries I know of are located outside of Tokyo. However, I can't definitely say "there are no micro-breweries in Tokyo" as I am not omnipotent.
Again, there are a ton of places to get micro-brews in Tokyo; here is a restaurant that I have frequented over the past years that serves Japanese micro-brews exclusively: BanKan
BanKan has 14 taps of Japanese micro-brews and they rotate their offering frequently; whenever a keg runs out it is replaced with a new brew. A pint runs between 900 to 1400 yen and the current offering is here. Notice that the prefecture the brew comes from is listed as well.
There are many craft beer pubs in Tokyo.
But there is no craft beer brand made in Tokyo.
I recommend COEDO BEER in Kawagoe-city, Saitama-Pref.
Kawagoe is a traditional town near Tokyo. It takes 40 minutes by train from Shinjuku/Ikebykuro. COEDO has 4 flavors, "Kyara" (Golden Brown), "Ruri" (Blue), "Shiro" (White), "Shikkoku" (Black) and "Beniaka" (Red). Especially, "Beniaka" is made from sweet potatoes in Kawagoe. Kawagoe is famous for sweet potatoes.
And "COEDO" means "Little Edo". "Edo" is the old name of Tokyo. Kawagoe has still old Tokyo street.
Please come and drink up!
On my 2nd trip to Tokyo, I found Popeye pub in a quaint part of the city @ Ryogoku: http://www.tripadvisor.com.sg/Restaurant_Review-g1066459-d1216476-Reviews-Popeye_Beer_Club-Sumida_Tokyo_Tokyo_Prefecture_Kanto.html
They have 70 taps and mostly from Japanese breweries.