That's what Brownstoner's reporting. Evidently, according to a source within the state Department of Environmental Conservation, which must sign off on development on the Gowanus site at Third Street and Third Avenue, the store's a no-go. Besides:
[E]vidently the trend in the supermarket biz has swung away from superstores, our source notes; in addition, in the wake of poor earnings this summer, Whole Foods announced that it would be cutting back on the number of new stores next year. The likely upshot? Even if Whole Foods decided to open a smaller store in Brooklyn, says our source, it's unlikely it would want to use this site.