I was taught that interrogative pronouns are always treated as masculine - i.e. "pwy" would always be "y gwaetha", never "y waetha". Even if the referent is known to be a woman. Is that not so?
If the group of people concerned are all female then elements in the question referring back to pwy could be in feminine form, but otherwise they would take a masculine form. So, Pwy yw'r waetha? would indicate an all-female group from which you were picking 'the worst one'.
In this example, Pwy yw'r gwaethaf? is also accepted, so stick with that if you prefer.