If you've been following Surviving in Japan for a while, you've probably seen me mention places to find certain health-related items, such as natural and organic food and such. iHerb is one of my personal favorites, but some things can't be imported to Japan, such as almonds and chia seeds.
I've attempted to list several places you can find these items (yes, almonds! yes, chia seeds! yes, hemp seeds! yes, raw food!) in Japan in the Metropolis article I've linked to below. If there's anything in particular you want to find, let us know.
Wholesome Holiday: Find your natural foods this Christmas | Metropolis Magazine
Summary of stores to find natural and health food items:
Tengu Natural Foods
Living Life Marketplace
Hemp Kitchen - for hemp items
Cocowell - for coconut items
Natural House - also has actual stores around Japan
iHerb is an affiliate link, but you get a USD$5-10 discount if you use it (from their advertising budget). I highly recommend iHerb for natural foods, health products, vitamins, supplements, and more. I've used them since my first year in Japan over four years ago and they've been a wonderful resource.