Baer did better against bigger fighters who didn't have significant speed advantage. He was also much more durable. It's possible that Cooney wears him down with power shots but it's unlikely. Baer would likely stop him, not without problems but that's the most likely outcome.
Baer has the better chin, but Cooney's hook to the body was devastating. I'm going with Cooney by early ko in an exciting fight.
Gerry Cooney equals modern fighter who fought modern fighters. Baer equal primitive fighter who fought in a primitive era. Cooney by early knockout.
Even if that was true, Cooney never beat anybody who was world class at the time of the win. There is nothing to argue for a Cooney win being the more likely outcome.