Just concluded my shopping for badminton stuff in Tokyo.
I would say, badminton is not a rather popular sports in Tokyo, it's behind tennis and (Japanese) soft tennis.
Prices are similar across many shops. Most major badminton specialty shops can be found near major train stations, like Shibuya, Shinjuku, Ueno etc...
There is also a major sporting shopping area in (御茶ノ水) Ochanomizu train station where they sell every sports goods under the sun you can find, i.e. golf, skiing, hiking, camping, tennis, etc.
A Mizuno boutique shop that have the complete range of badminton, tennis and soft tennis stuff.
Racquet brands are rather limited, mostly common Japanese brands like Yonex, Gosen, Toalson, Kumpoo and foreign brands like Prince, Wilson and Babolat. Li-Ning is rare and Victor is non-exsistant.
Shoe selections are wide, but as Japanese players have rather small feet, size above 28cm is very difficult to find. Ditto for socks, with size limit up to 28cm.
Badminton bags however are a different story, Tokyo has a good selection of Badminton bags.
Otherwise, customer service is very good.
Prices are fixed and rather high, but the good thing about Japanese products is quality; you get what you pay for!