Hi:)
First, why are you looking for wholesaler markets?? Because it's cheaper? Otherwise for business??
Well, those below are not markets, but have lots of staitionery and other cute stuff which are good for souvenirs.
Shimojima
http://www.shimojima.co.jp/eng/index.htmlNot a market, but you can find lots of stationery at much lower prices.
Daiso
http://www.daiso-sangyo.co.jp/english/You can buy almost everything at 100 yen there! It has stationery, sweets, foods, character goods, daily stuff etc. though the quality is sometimes not good. Daiso in Harajuku may be the biggest in tokyo. Very popular among japanese and foreigners.
Don Quijote
http://www.donki.com/index_en.phpA kind of cramped supermarket. You'll really feel cramped! lol
It has various stuff at lower prices. Cosmetics, toys, sweets, charater goods, alcohol, cheap clothes etc.
Suited for young people.
Loft
www.loft.co.jp/
Has various stationery and daily things at fixed prices. Just fun to see!
Loft in Shibuya is the biggest in tokyo maybe.
Ito-ya in Ginza (main shop)
http://www.ito-ya.co.jp/index.htmlHas about 10 floors, and each floors have lots of stationery at fixed prices. Whenever i go to Ginza, I go there!! The one in Ginza is the biggest.
That's all from me who love stationery!
I hope you'll have a great time in Japan.
All websites don't have english version, but you can ask concierge and police where they are.
Take care!