When NT4's kernel was released and Linux was on 2.2, there was a good reason to choose Windows for stability - or at least, there were trade-offs that were acceptable up to Windows 2000. After that, it became a battle for libraries. If you're using C# or other dotNet, then you're on Windows (or Mono?!?), otherwise your platform is Linux.

Both are reasonably capable of high service uptimes and solid performance. With Server Core and PowerShell, there's a lot more parity than my fellow Linux admins want to admit, but either is a viable choice for general IT services at this point.

Note - I'm excluding licensing entirely from this, as well as infrastructure maintenance and control surfaces. Nobody likes DSC, and there are several superior config management solutions for Linux that don't have meaningful analogs on Windows.