I don't think anybody tells Merlino what to do, if NYC had their way, Merlino wouldn't be boss. Joey only listens when Thiers money involved like any boss would

"McGurn likes you, so I make you. So you are now one of us, if you fuck up, we take it out on McGurn. He is your sponsor. Fuck up, it's his ass. You work in his crew, he is your capo."