Both languages get compiled into IL code (otherwise known as “.NET binary dll’s”) by the mono.exe compiler (not the web player).
So from that point of view, it does not matter. In fact, you can use any language that compiles to a IL binary. Boo, VisualBasic, F#, IronPython, BrainFuck, whatever…
That said, there could still be reasons to choose the one language before the other:
- If you are firm in one of the languages, choose this one.
- UnityScript is an order of magnitude slower to compile than C#. So you might not use it solely in a project with 100k lines of code.