I can't tell you if "the germs" are still lurking. That may depend on how messy your bathroom is! If he was neat, probably no big deal. But you should still clean.
If he was disgustingly negligent of where to put the vomit (this happened a few years ago with my nephew - YUCK, the little slob who @ 11yo should be able to handle lifting seats and good aim), I think you'd want to give a good clean. Regardless of whether it's "germy" or not!
If you do need to clean a disgusting place, I'd recommend putting on rubber gloves and using serious cleaners like Comet and ammonia, etc., then Lysol. That nice 409 stuff is for touch-up. Use just paper towels to throw away, or be willing to chuck the rags/sponges you use.
The good news is it's been 3 weeks, and you haven't shown any signs. People are most contagious BEFORE they "get sick". You're actually safer being around your uncle actually sick than the days before when he seemed fine. I always give myself a week from when the person was 1st sick to see if I "get it". Then I feel safe.