Do you mean if a PhD from a higher ranked institution is potentially better?
The answer is: it is better the one which has the potentially better supervisors/equipment at the field of your interest. An institute being more prestigious does not guarantee that will have the best personnel at the area of your interest.
Do you mean which one is better in terms of the quality of the graduates and the prestige in academia?
This depends on the actual research of the student. Many stellar students go to the best institute and they don't produce anything for one reason or another. At the end of the day, in academia, what would matter would be the actual content of your demonstrated research and not the particular institute/university.
In short: actual research is ranked higher than institute. Having saying that, in case of ties, these are sometimes broken by the fame of the adviser and/or institution/university.
So: NO, an institution is not better a priori since there are many variables to consider. It might be better in cases where what matters is the place of PhD (but I cannot think of any such scenario).