I like them both, and I own them both in some form. I shop at Sprouts, Costco, and NGVC mostly, but I will go to the local WFM and buy things occasionally. I really like their free samples, and I also eat lunch at WFM on occasion.
Natural Grocers is more of a pure play on organic. I don't buy "conventional" GMO & pesticide/herbicide riddled products, so Whole Foods doesn't do it for me. I'd prefer to buy at and invest in a company that "walks the walk." I think NGVC's smaller totally organic stores are a big advantage. I don't see Whole Foods as much different that Krogers whose stock is half the price. Whole Foods' just doesn't compete on price or marketing (one page sales flyer with maybe one or two organic items) compared to Sprouts' or NGVC's magazine type flyers.
"I don't see Whole Foods as much different that Krogers whose stock is half the price."
I presume you meant Kroger's PRICES are half of WFM? KR is valued at a bit less than twice WFM.
As far as marketing, in my area, WFM does do some radio advertising...AND they have a magazine type publication they turn out monthly or so; it contains coupons, articles and recipes, nice photos and employee profiles.
IMO, WFM does "walk the" talk. WFM has never professed to be an organic outlet, but one that sells natural and organic items. WFM is a positive for its neighborhoods; donating to local "causes".
I don't have the luxury, such as you, being able to choose which nat/organic food store to shop at. I've only WFM and TJ's.