I think Jimmy was a rat. When Silvio and Chris had him at gunpoint where they taunt him by saying he should call for help on his microphone(wire), Jimmy never denied it so it is likely that he was an informant. When Jimmy is about to be executed, his reaction is more "Oh no!". I figured if he wasn't a rat, he'd be denying it. Given that he said "Mother of God", and "Oh my God" under his breath in a serious way and didn't deny being a rat when he was at gunpoint, it likely was true that Jimmy was an informant.

Plus the other reasons to support my suspicion include the questions Jimmy was asking Tony about the Colombian heist in the basement after his release, his quick release from jail on bail after being busted when the FBI finds a pool table full of guns and Jimmy had other charges already against him as Tony alludes to, the meeting with the admin/capos where it is apparent to everyone else Jimmy is acting odd, and when Jimmy was trying to get Junior to talk about the Brendon hit is another tipoff.

But this is one of those David Chase things we will never know as it has never been explicitly revealed whether Jimmy was a rat or not.