First off, I don't think Macs are "the best." It's my preferred choice, but that's it.
The OPs question is somehow funny, and being a scientist myself, I feel like contributing to the discussion.
1. Scientists don't always get to use "the best" equipment. In many cases, they have to make use of what is available or what fits the budget. Many universities and labs also have special contracts with PC vendors.
2. The choice of hardware is often determined by the software. Whatever is prevalent in a certain sub-field can easily dictate the OS most people are running.
3. I'm really not sure that science documentaries provide a good cross section of what is being used by "real scientists."
On a side note, the high energy physics community (those guys that discovered the Higgs boson), is quite Mac dominated. However the systems that actually control the experiments are mostly Unix based. The majority of my colleagues uses Macs, but certainly not all of them. Quite a few are happy with windows, other are happy with the endless struggle of a working Linux distribution on their Windows PCs.