I am looking for an efficient way to determine if a set is a subset of another set in Matlab or Mathematica.
Example: Set A = [1 2 3 4] Set B = [4 3] Set C = [3 4 1] Set
I think the question you mean to ask is "given a list of sets, pick out the set that contains all of the others". There are a bunch of edge cases where I don't know what output you would want (e.g. A = { 1, 2 } and B = { 3, 4 }), so you need to clarify a lot.
However, to answer the question you did ask, about set containment, you can use set difference (equivalently complement wrt another set). In Mathematica, this sort of thing:
setA = {1, 2, 3, 4};
setB = {4, 3};
setC = {3, 4, 1};
setD = {4, 3, 2, 1};
Complement[setD, setA] == {}
True
indicates setD is a subset of setA.