M5 Goku must be at least 2x than 5th Cooler, considering he shrugged off a blast of his. Considering this
Goku has to be weaker than Androids Saga Goku, who's not amazingly different from his 3 year prior self, i
place 5th Cooler at Mecha Freeza level. Namek Goku has a chance, but not much.
I have Cooler equal to Mecha Freeza and ever so slightly stronger than Goku. The slight power advantage coupled with haxed Supernova would give Cooler the win in my opinion.
Movie 5 appears, to me, to be an alternate dimension where Goku went straight from Namek to Earth and didn't stop at Yardrat on the way, thus never learning the Shunkan Ido technique or how to harness Super Saiyan. It would also help explain the total lack of android/Trunks mentions.
With that said, Cooler would still do work on Goku. Goku is more or less in between his Namek and Yardrat selves in my opinion, and unlike some others, I don't have Cooler at a monstrous disadvantage in the movie.