I've observed the same as you; it's like Whole Foods in having good foods but at higher prices.
Farmers markets support local farmers but I don't know if there's one in your area. Those two stores may too, but are also more national (perhaps some hedge fund owns them).
There's a farmer's market and a food co-op also in Chestnut Hill but they don't always have what I'm looking for. They're also pretty pricey because Chestnut Hill is just that kind of neighborhood. The Acme a couple blocks from me usually has very poor fresh fruit and vegetables. I generally shop on my way home from school at a TJ's that is sort of on the way, but since I haven't been teaching this semester that hasn't happened as often. Mind you, I'm not complaining - it was fun to find another option within walking distance.