Have you taken a look at department stores?
They are handling the top quality ones, though they tend to be pricey.
For example:
Mitsukoshi (Ginza) : 8F
Isetan (Shinjuku) : 5F
Seibu (Ikebukuro): 7F
or those special stores
Tokyu Hands (Shibuya): 3C (*They have three different levels for each floor)
Loft (Shibuya): 3F
And recently opened mall Hikarie in Shibuya has THE CONRAN SHOP KITCHEN, their "first single-concept-shop", according to them. It's on the 5th floor.
If you go to supermarkets, they are mostly selling cheap Teflon stuff. The stores I've listed are handling good cast iron pans (such as Le Creuset and Staub - both are quite popular here), as well as stainless steel pans and so on.
As an alternative for non-stick pans,you might want to look for Silver-stone wares too.