One of the hyped elements of this season by the showrunners is that we're going to see conflict in the crew, including between Picard and Riker. That would be false if Riker was brainwashed by an alien. The conlfict wouldn't be between Riker and Picard, it'd be between the alien and Picard.Problem is they wouldn't have a beef with Picard or the TNG crew. I think it's look most likely to be the "Conspiracy" aliens. I got a theory I don't like but I think RIker might have one of them inside of him. Maybe even Shaw.
Furthermore the aliens in Conspiracy were only invented because Gene Roddenberry did not like the idea of evil Starfleet conspiracies and insisted they were brainwashed by aliens to get the story aired. The showrunners said they wanted to have more drama this season and push the boundaries of Gene's 'no conflict in Starfleet' ideas. It'd be very ironic if they went back to the alien parasite plot device designed to appease the no conflict in Starfleet idea in the first place.
Due to all of the above, I find it very unlikely the Conspiracy aliens are controlling Riker and Shaw.