You can use the speedns or healthkoreaus websites if you have an ID card, which requires a Korean National. Basically, get a Korean to order for you. Very reasonable prices. Other than that your best bet is actually iherb IF you have an Alien Registration card if your own, that will allow you to have such supplements shipped at a reasonable cost. An alien registration card however won't allow you to order from Korean websites.
If not numdaemoon market in Seoul is pretty much your only option. As people said in the basement , it's the foreign food section. It's on subway line 4 at Hoehyeon Station. I am not sure of anywhere else outside of Seoul, and I lived in Seoul and surrounding Satellite cities.
Kyotto, where can you find such items outside of Seoul? Even GNC only sold protein at 150 000 (150 usd almost) for a little 5 tub of whey protein.