Just returned from Vieques. Yes, I did see one store that was a "natural foods" store. I think it was probably more like a health food store. I didn't see too many cows, goats or pigs on the island, but the chickens were everywhere. I would say they were free range chickens/roosters, just running loose everywhere. Vegiterian meals can be found in just about all resturants. We did hit a farmers market on Tuesday, but it was pretty bare, not much is actually grown on the island as far as I could tell.
Hopefully you have already rented a car and don't be afraid to take it off the paved roads.
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