My impression is that neither cyberocracy or cybercracy is really well-formed in the context of classical languages, so you can just pick whichever one you feel sounds best or that you think is better formed according to English analogy.
According to the Oxford English Dictionary, the modern English prefix cyber- was formed by detaching the first two syllables of cybernetic(s), from Ancient Greek κυβερνητικός (kubernetikos) which comes from the verb κυβερνάω (kubernao) (this is related to the English verb govern). So I don't think there is really any "etymologically" correct way to use cyber- as a prefix any more than there is an etymologically correct way to use -holic as a suffix.
If we set aside etymology and just look at modern English analogy, there seem to be two competing tendencies: cyber- is used as a prefix in a lot of words, and cybero- is not; but -cracy is preceded by -o- in a lot of words, and is not directly preceded by r in any well-established word. (Urban Dictionary does record two innovative formations that end in -rcracy: hypercracy and twittercracy.)
I think I prefer the sound of cyberocracy a bit because its stress pattern seems more natural to me: the first syllable of "cyber" is stressed, as in many other words, and the third-to-last syllable of "ocracy" is stressed, as in many other words. With cybercracy, we have to put a single stress either on the first syllable, which is earlier than words ending in -cracy are usually stressed, or on the second syllable, which would cause "cyber" to have an unusual stress pattern compared to other words starting with this prefix.
Other alternative formations are possible. If you search Google for "cybernetocracy", you can find a few hits, and "cybernocracy" is common enough to have made it into the Oxford Dictionaries.