Lexington Food Coop in the city always had good food. I don't think it is actually a coop anymore.
Lexington Co-operative Market
In summer, there are Saturday or Sunday farmer's markets in many towns; I go to the one in Alden on Broadway and the one on Main in Clarence. They are open air markets set up in lots and not there from Oct until about May.
The food terminal where stores go to get their food is on Clinton Ave near Bailey in the city. You used to be able to go there any time. The area is kind of rough.