If he’s living under your roof, he should expect to obey your rules or deal with consequences, at least on the surface.
Bodily autonomy and the right to make one’s own medical decisions certainly come into play, too. But I confess I have very little sympathy for a person who has no legitimate contraindications to the vaccine and simply refuses to get it. A very selfish choice.
You can’t force a legal adult to get a medical procedure, but you can absolutely refuse to have him breathing plague particles on your surfaces in the future. IMO, considering the number of preventable deaths in this pandemic, you would not be unreasonable to say, “get the shot, or get your own place once you graduate.”
Easier said than done, of course. It’s a tough situation.