Ok, I'm not sure where the confusion is coming from here. He was a rat. They couldn't have made it more clear that he was a rat unless they had Tony show up at his house and find HIS actual wire too.

He's out on bail for conspiracy and gets arrested with a pistol on him and they find a whole bunch of machine guns in his club. Yet somehow he's able to get released.

He gets out and immediately goes to Tony's house and starts asking him some very suspect questions, trying to bait Tony into talking about past crimes including murder. Even after Tony flat out ignores his questioning he goes back to it and tries to get him to talk. Tony's reaction to the questioning, his comments to Jimmy and the camera work is more than a suggestion to the audience that Tony is aware of what's going on.

Calls a meeting with the capos to discuss old business.

Tries getting Junior to talk about the murder of Brendan Fillone.

When he gets ambushed by Sil and Chris and they let him know they figured out he's a rat he doesn't say "What the hell are you talking about?!?!?" he says "Mother of God!" something one would probably say if they knew they were found out and about to get shot. The game was up at that point and he knew it.

Jimmy and Pussy were both rats, we just got to see the actual reason that Jimmy flipped and everything that happened with Puss was off screen. Ray Curto, Jimmy, Pussy, Adrianna, Gene, Febby, etc. There were a few rats in the NJ crew. As far as Skip's comment about Jimmy eating the bullet for Puss, that's true he did. But that doesn't mean he wasn't also a rat. Wouldn't make much sense for the FBI to let other informants know about one another for obvious reasons. Gene didn't know that Curto was a rat and they don't confirm it for him when he asks either. And we never find out why either one of those guys were cooperators either.