If I'm not mistaken (but I often am), the physicists already have a rather simple way of defining the center of mass. But I don't think you can do it with just sets. You have to associate a mass with each set. The critical axiom is simply the one we all know:
If $A$ and $B$ are disjoint sets with masses $m(A)$ and $m(B)$ and center of masses $c(A)$ and $c(B)$ respectively, then the mass of $C$ is $m(C) = m(A) + m(B)$ and the center of mass of the set $C = A \cup B$ is given by $$ c(C) = \frac{m(A)}{m(C)}c(A) + \frac{m(B)}{m(C)}c(B). $$
You do need one more axiom to get started somehow. I believe physicists like to start with point masses (where the definition of the center of mass is easy) and then view a body as a limit of point masses. That's more or less what Liviu has proposed. But it also suffices to say that the center of mass of a square or cube is its geometric center. Or, more generally, the center of mass of any set with sufficient symmetry is its center.
Of course, if you really want arbitrary shapes, then you do need a countable version of the first axiom. But I think that's all you need. Note that this approach allows for bodies with different and even non-constant mass densities.