You’ve got two questions here, the one you asked, and the one that prompted you to ask. On the one that prompted you, I’ll only point out that Archimedes should probably be one of those top three people, and he wasn’t this most recent millenium.
That said, though, on the statistics: We’re given that only 1 person in 16, historically, has been a European male (I’ll trust your research on that, but it doesn’t seem too unlikely). The first question is “Assuming no correlation between European male-ness and physics success, how likely would it be that the top three were all European males”. The top physicist would have a 1 in 16 chance to be a European male, the #2 one would have a 1 in 16, and the #3 one would also have a 1 in 16 chance. If we were to assume that there were no correlation, the chance that all three would be European males is 1 in 16^3, or 4096. This is, as you recognize, a very small probability, which would tend to support the conclusion that success in physics is, in fact, correlated with being male and/or European.
To your second question, given a set of 16 physicists and assuming no correlation, what is the chance that at least one of them would be a male European? This one is easiest to do by considering the opposite case: What are the chances that none of them is a male European? The first one has a 15/16 chance of not being a male European, the second one has a 15/16 chance, and so on. So the total chance that none of them is a male European is (15/16)^16, or .35607… Incidentally, this number is very close to 1/e, and will get closer as you take larger numbers: (99/100)^100, or (99999/100000)^100000, etc. But anyway, the probability of none of them being a male European is .35607…, so the probability of at least one of them being one is 1 minus that, or .64393…
Finally, a caveat: You have to make sure not to cherry-pick your data. If, before collecting your data, you ask “How many of the top three physicists are European males”, then that’s one thing. But if you look at the data and then say “The top three physicists are all European males”, that’s another. Suppose, for instance, that the top 3 were Europeans, but numbers 4-23 were all from India. In that case, if you wanted to make Europe look like the home of physicists, you could decide after the fact to just focus on those top three, but it would be very deceptive to do so. This probably isn’t a big issue in the specific case you’re asking about (I suspect that any way of analyzing the population of physicists will end up showing a bias towards European males), but it can be in general, in statistical debates, and it’s something to look out for.