It all actually depends on what you need. I would say that these two programs cannot be compared side-by-side, because they belong to two completely different groups.
The Cocktail application is a tweaker, not a cleaner program, which CleanMyMac is. Lots if Cocktail's functionality just duplicates inbuilt MacOS X resources, however, Cocktail makes it just a bit easier to tweak the system by doing that from one application with quite a geeky usability and utility-like interface. Just in addition to all that it can clean caches and logs.
Speaking of CleanMyMac, the best explanation will probably be that it is a complex cleaning solution for Mac OS. Its functionality is aimed on precise cleaning of the os and it works not only with logs and caches, but with literally everything you can safely remove from a Mac and make it a bit faster. Moreover, the interface, as well as the usability do belong to the top rank applications.
In your case it will just be a great addition to the applications you already have, not a replacement of Cocktail.
I have the latest version of Cocktail for my iMac which I use weekly. Now I see CleanMyMac being offered. Is CleanMyMac a better app for taking care of Macs?