Unity’s JavaScript is a lot like Flash’s ActionScript, so that’s probably your best choice as a Flash developer. Most of the examples are written in JavaScript, which makes learning easy.
I prefer C# myself because I come from a Java programming background and the two strictly-typed languages are quite similar. But there really isn’t a “best” language, and you’ll find that both are used heavily. It all comes down to personal preference. Also note that both C# and JS scripts can be used in the same project.
On the same topic, are there any major speed differences between using C# and JavaScript? I would have thought C# would be more efficient and therefore quicker to execute, but is that not the case?
No, they’re both compiled down to the same runtime code. That said, C# is more strict on syntax by default, so you’ll probably end up with less dynamically-typed variables by necessity.
However, if both your script in JavaScript and your script in C# was exactly the same (aside from syntax), they should run just as fast as each other.