Down to Earth is going to be your best bet for organic food or specialty ingredients such as nut cheese, tahini, etc.
Safeway has a bigger produce section, but you will find much less specialty foods.
Costco has a good produce department, but you may not be able to find very basic ingredients. I just got back from the Hawaii Kai Costco and they didn't have strawberries *boo* Last week, they didn't have cabbage. The Costco stores here are very big on salad mixes.
Down to Earth and Costco are a block away from each other. Safeway is at the opposite end of Kapolei, which can be a 30+ minute drive during peak traffic.