Rights can be said to have a real existence only to the degree that society dictates, and only in a social context. Your will is not inviolate simply because you choose to frame it as a right. So the first answer to that question is that it must first be established that this is some sort of right that society has agreed to respect, and secondly you would have to take on the issue of the harm to society in order to argue whether the one or the other was more important.

Vaccinations are indeed something of an affront to one's physical person. So is collecting DNA evidence. I think that you will find upon further reflection that the physical integrity of one's body is not much affected by a vaccination, and that personal liberties do not extend to causing grievous bodily harm to others.