I guess it depends on what you go for. Whole foods does have a nice bulk section.

I tend to either get my produce at Costco, farmer's markets, or at Korean grocery stores. Usually nothing can beat the selection & prices on the latter. Costco's great if you want 5 lbs of organic spinach for $5.

Whole foods has a ton of packaged prepared foods as well.

I hven't noticed a problem when looking for ingredients from scratch at Trader joe's, but I don't live near one, so I really just pop in when I get a change and buy a bunch of the dried fruit.