I think prime Cro Cop would win. Ngannou has not at all proved that he can deal with low kicks and Cro Cop is excellent at avoiding serious damage. He's also survived against and beaten the best of the best kickboxers in the world in their primes so his level of competition is SIGNIFICANTLY higher.
If you look at his record, the only people who KO'd him in his prime only did so due to the threat of the takedown so please, hold the MMAMath and actually watch fights before you dispute this.
Obviously, it's a HW fight and there is always a lot of risk but I would take the more well rounded striker who is better at keeping distance over the power boxer who has shown to mentally crumble when he doesn't get the quick KO.
Cro Cop via decision or late TKO