Speaking as someone who has achieved their MCSE and updated it twice of the past two decades, and currently holds certifications for RHCE, HP-UX and AIX. I can tell you this.
Windows has signficantly caught up with Unix in terms of reliability, and since most of us are running Linux, we are using similar hardware.
If you were using IBM pSeries or HP 9000 Series equipment, your hosting would be more reliable than anything budget Windows hosts could achieve, but we're not.
Linux and Windows reliability given a load they can handle are on par.
Linux does however, on average, use much less resources and appears to run more efficiently. This is taken from experience over decades working for many companies who have tried the same work loads on different platforms.
My particular affinity to unix came from studying computer science at university, where quite frankly what you could do with Solaris put Windows of the day to shame.
I do like windows, I've seen it mature, change it's kernel, scheduler and networking to become more and more like BSD Unix.
Windows is significantly easier to use and properly administer than Unix, which is a little freehand in it's configuration. With Unix's freedom to do things the way you want, comes the ability to really screw it up badly.
I don't think Linux can run windows apps at all well.
Windows on the other hand can run opensource PHP apps either through IIS or even apache or nginx, it can run varnish and everything than Linux can do, because the open source tools are available on windows.
All of the opensource tools are also efficiently coded, so will run equally well on windows.
I don't believe however that many people are running the open source tools on windows as hosts (other than for development) because their would be no point installing windows just to be the kernel for the rest of the GNU toolset.
I believe whether you choose windows or Linux should be down to what you are comfortable installing, configuring and troubleshooting.
At UnixGuru, we have a poster on the wall saying "Don't sell, what you can't support" it's no good bespoking everything, as the quality suffers. Design well made building blocks and base your solutions around those blocks.
So if you have trained for Windows and have experience with windows, choose windows, the same goes for Unix.
Whilst I own UnixGuru hosting, I leave my staff to run the business and consult for other businesses. I work with online retailers who are scaling up for Christmas (using only Linux), Banks performing stocks and money exchange systems (using Windows and Linux), and a well known Orange airline, who use ALL windows systems.
I tell you this, the traffic handled by those windows boxes for the airline is phenomenal, so windows does scale.
I don't think you can say one is better than the other.
For budget hosting Windows doesn't support CPanel, you may be pushed down the plesk route. I think plesk is a pain in Unix, as it rewrites all the confs if you so much as breathe on your keyboard.
You should first consider what you want to achieve, what you budget is, what you know and what you need to know and then make your decision.
(Sorry for the waffling).