It really comes down to what the experience level is for the people that are going to end up supporting the instances. 'Better' is quite subjective in this case.
Personally, I would choose Linux, only because that's where the majority of my administration experience lies. Also, just anecdotally, the vast majority of JIRA instances out there run on some flavor of Linux, (I can only think of a few that run on Windows).
Just my $.02.
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