Cotto is the better fighter in my opinion as Vargas was juiced to the eyeballs in his prime. They were not in the same weight class when they were prime but Vargas was KO'd by a lot of smaller guys in Oscar, Tito and Mosely so I think Cotto would also be able to knock him out.
At 154 Vargas wins he's too big and strong at the weight. Cotto's best weight was 147 he wasn't as effective at 154 going 5-3 overall with mixed results.