They're both used, so anything more specific than that would depend on the unit itself. There's a number of other models of the M249 that are also used as well - the mk II and para aren't the only versions of it kicking around.
As for what's better...that's all relative. What will you be using it for? If I'm sitting in a prepared position and just have to sweep back and forth between a left and right of arc, I'd take something with a longer barrel and full stock (Mk II, Mk 46 or even just the plain ol' M249). If I had to jump out of a plane with it, I'd probably take the E3 or E4 because it's a lot shorter and easier to move around with.