Well generally yes, if you are doing painting, you can factor in a rough painting time as well with:
var start = +new Date();
//Do dom methods draw to canvas etc
setTimeout( function() {
   var stop = +new Date();
   console.log( stop - start - 13 );
}, 13 );
Also, make sure you call each test as a function and warm-up the functions before timing them instead of doing the code in-line.
function test1() {
    //ops
}
function test2() {
    //ops
}
var l = 1e5;
while (l--) {
    //warmup
    test1();
    test2();
}
var start = +new Date();
var l = 1e5;
while (l--) {
    test1();
}
var stop = +new Date();
console.log(stop - start);
var start = +new Date();
var l = 1e5;
while (l--) {
    test2();
}
var stop = +new Date();
console.log(stop - start);
You should note that this setup invites JIT optimizations (which is why it was done in the first place) so you should look out for dead code elimination.