P.M.
Offer milk & juice in the sippy cup and only water in the bottle. If it's milk she wants, she'll learn real quick that it simply isn't availble from the bottle anymore. If it's the sucking action she needs, she may begin to rely on her pacifier or thumb (whichever she prefers) while she makes this transition.
With my kids, I explain all changes before making them. Even though they might not entirely understand, they do tend to be more cooperative when I remind them that this particular change was coming. It's especially effective if I tell them that the doctor said so :)