Haha you'd be surprised. He would actually do pretty badly, except on the straight up Physics questions. Their understanding of chemistry and biology was much different than ours, and in fact Newton spent most of his life trying to turn poo into gold.
That's right, he was a committed alchemist. In fact, he wrote over a million words on the subject and considered it more important than his other stuff (you know, minor stuff like inventing a whole branch of mathematics so he could invent a whole branch of physics). Now, of course, we know that you cannot just change poo into gold by heating it up or some such nonsense (he had no idea of atoms, which might prove to be a bit of a hurdle in modern chemistry and organic chemistry).
He would have trouble with the VR section as the new vocabulary and the change of grammatical style that has crept into the English language over three centuries.
Of course, that doesn't say anything about his intellect. Obviously, he was smarter than any person on this board, or alive today, and probably one of the three smartest people to have ever lived (along with Archimedes and Einstein). But I doubt he would do well at all on the modern MCAT.
Now if you are asking how he would do after he had a couple years to 'catch up', then its a different story.