ES6 Set equality test

seteq.js

function seteq(a, b) {
  if (a != b) {
    if (!a || !b) { return false; }
    for (var e of a) {
      if (!b.has(e)) { return false; }
    }
  }
  return true;
}

var assert = require('assert');
var s1 = Symbol(), s2 = Symbol();
var a = new Set([s1]), b = new Set([s2]);

assert(seteq(a, b) === false);
assert(seteq(a, null) === false);
assert(seteq(null, b) === false);
assert(seteq(null, null) === true);
assert(seteq(null, undefined) === true);

a.add(s2);
assert(seteq(a, b) === false);

b.add(s1);
assert(seteq(a, b) === true);

A check that the sets are of same size would greatly help your comparison's accuracy without needing to loop over them in the case they have different numbers of items.