I believe its Minelli because of several things.
The first one that jumped out at me was in the flashback episode to Jane joining the CBI.  Minelli seemed very keen to have Jane on board.  And that phone conversation he had with Agent Shultz, where she said it would be good to have a friend in the FBI. Red John has said himself he has a friend in the FBI so that may be it.
The other thing is his age.  RJ has to be older than Jane given the time the murders started and when it was said he was the friend of Dumar's father. Minelli looks to be right around the right age.
RJ has found it very easy to access CBI network servers.  As the boss and former boss, Minelli could very well still have access to do things like upload the vido of Agent Darcy.
Lastly is the easy way that he left CBI. This has left him plenty of time to do the things RJ does, whether that be murders or turning new followers.