During the first five Harry Potter books (or movies) I always felt that the potions class was the most like our muggle science classes. They learned what different potions and materials do, where they come from, how they’re made. There’s a strong hands-on part, like lab work, where method is important.
As a result, I considered Snape to be “the scientist” in the book.

But during book 6 (Harry Potter and the Halfblood Prince) I changed my mind. It wasn’t just Snape’s dubious after-school activities, but my own opinion on what makes good science had changed a bit in the mean time, and two of the books’ characters had developed to fit exactly what I now valued in science: Fred and George Weasley!

Even though they couldn’t stand the school environment, they’re hard workers and unlike most of the characters they’re creative. They know what they want to make (eg. something that makes you sick just long enough to cut class and then feel better) but they’re open to different ways of reaching their end goal, and they’re willing to adapt their recipes if things don’t work out.

The potions classes have always leaned on following a given recipe exactly, and as a potions teacher, Snape followed the book and never allowed for alternate solutions. However (spoiler alert!) at the end of book 6 we do find that he is far more creative than we’ve ever given him credit for so far. He improved on all the textbook protocols when he was still a student! We’re probably supposed to conclude that he is a much stronger wizard that we’ve ever thought, but it was at that point that I redeemed Snape as a scientist. He did have the mind for it! Unfortunately, he would be most horrible to work with. He would be the kind of person that will never admit that a hypothesis was wrong.

So, in the end, I’m sticking with the Weasley twins as my choice of “Best Scientists”, but Snape is still a very close second.

I asked people for their comments (here and here)

I was glad to see that Fred and George did come up in comments as well, so I wasn’t the only one. Snape was obvious.

What I have always completely overlooked, having been so used to science=lab and science=chemicals, was that the Herbology and Care of Magical Creatures classes were also somewhat scientific. So Andrew’s suggestions of Neville (as a botanist) and Hagrid (as an animal care technician) are right on the mark!

Minds were split on Hermione and Luna. Maxine says Hermione would make a good scientist and Luna a bad one. Someone going by hpreader says the exact opposite.
I would argue that neither of them would be very good. They’re both very smart, but each of them has one of the characteristics that give me problems in the lab over and over again, and they’ve got it much, much worse: Luna is way too distracted, and is having too much fun thinking about other things. If she was a researcher, she would create a hypothesis and not bother to test it, because how could it be wrong? Hermione is too attached to the way things should be according to the book, and can’t see that there might be other ways. This is extremely clear in book 6, when she gets mad about Harry doing better than her when he is not following the official potions book. How can her work be less good if she’s following exactly what’s in print? As hpreader says, she isn’t creative enough.