There are thousands and thousands of farmers in the US, and millions around the world. There are certainly more sources of food items than retail outlets.
even the most hipster eco hand made brands in wholefoods are most likely an off brand of nestle or uses their products as main ingredient and doesn't list it as such.
You mean hipster eco hand made brands like raw ingredients, such as Eggs, Vegetables etc.? Processed food is unhealthy for the most part anyways, so it is better to avoid it.