Besides that, the larger legit business provided a great cover for the smaller illegal business. He didn't need to run the grow op to run the cherry factory, but he did need the cherry factory to run the grow op more easily. There's no way he could have run it undetected for at least six years in the heart of NYC without the cherries on top.
I suspect that the cops had access to illegally obtained evidence, and the bee thing was the only way they had to legitimize what they already knew.