I shop nearly 100% at Community Natural Foods. They consistently have IN-STOCK the products that I use/need. Their produce section is miles-above anywhere else that I have tried in the city.
If they run out of something, it's in stock within 1-2 days, normally.
I wish that they had a bit more of a local focus but it's still possible as long as you are willing to read labels in-store to find out where things are coming from.