I am not a professional teacher but my answer would be "both", or, if you prefer, "either". Just like the drink itself, the choice is a matter of taste. "With" might be slightly more common, often paired with "or without?", but it's common to hear "and sugar?" or "and milk?" as well.
My God, how many teaspoons do you guys put in your coffee? I've heard of 'half and half milk', but a cup half coffee and half sugar?!
When asking, one usually says, 'With or without", meaning, do you want your coffee with milk (or sugar) or not.
I think the expression you might mean is, coffee with milk and sugar.