I think this is one of those things where you should do what the user expects.
What do they expect? Well that's sometimes the tricky thing to figure out. Eye movement studies have been done in excess to determine the best placement for the most important call-to-action buttons. And users often start in the upper-left hand corner. On the other hand, these window buttons are so ubiquitous and so familiar that they shouldn't require unnecessary thought. If a user is accustomed to an OS with the buttons on a certain side of the screen they will naturally be looking for them in that spot. Past experience is going to be the dominant factor in what the user expects.
So for example, if your audience is composed of 90% Windows users, I think you should absolutely put these buttons in the upper-right. Windows users will naturally look in the upper-right hand corner for these buttons because that's what they've been trained to do.
Or better yet, if you can adopt the built-in window controls (title and button placement) of the target OS, then it takes this decision out of your hands and the buttons will always be where the user expects.