There is not 1 correct answer to this one.
We have a lot of Windows and Linux hosting customers. Some prefer one OS over the other. Some base it on what language their site was built on. Some go with whatever hosting you already have.
Linux hosting is the most popular, because it is cheaper for the web hosts (no Microsoft License fees).
Mosts hosts charge extra for Windows hosting, other do not.
Really, it just depends on what your doing. Does you code need to run on one or the other?
Is your host going to charge you more for one or the other?
Are you more familiar with one or the other?
Only you can decide "which one is better" (for your needs)