OK, so I think LTrain's answer is correct, but perhaps DustinDavis needs an answer that is fleshed out into further detail in order to be satisfied.
Reasons Why the film indicates Donnie has collaborated with the FBI:
1. Edit Composition
The scene that immediately follows Jordan's final arrest begins with a shot of Donnie systematically erasing the files on his computer, looking nervously around the office. This is in anticipation of the FBI showing up at the office, as he is already erasing the data before they walk in. He could only have known they were coming if he'd had prior knowledge. If Donnie had found out about this impending raid through a source other than the FBI, and was as such still loyal to Stratton Oakmont, he would have shared this information in order to enable some kind of damage limitation procedure, or at least advised his brokers to do the same. The raid comes as a surprise to the rest of the company, or they are at least caught off guard, indicating they didn't know.
The only reason Donnie wouldn't have told them, is because he would have had to be forthcoming in how he obtained the knowledge of the premises search, which would have publicly outed him as a collaborator.
2. Jordan's Reaction to seeing the post-it note
This scene is ultimately the moment that Jordan finally does become 'The Hypocrite' he was fearful of when talking to Stratton Oakmont employees, the moment when he gives in. It's not neccesarily prompted by the fact that the FBI has incriminating evidence on his contempt of court (that sort of litigious impropriety has failed to phase him at all so far), but by the realization that he is alone, and has no-one left.
He immediately realizes, as we the audience are in turn supposed to , that the only person who could have submitted the post-it as evidence against him is Donnie, meaning his best friend has ultimately betrayed him in order to cut a deal with the FBI.
Jordan doesn't argue, or resist, or question how they obtained the note, because he knows, and this is the catalyst that ultimately provokes his surrender.
3. That the post-it is even Admissible as evidence
A piece of paper with the words "I'm wearing a wire. Don't say anything incriminating" would not be sufficient evidence to hold anything together in a judicial court, without a witness to explain the context of it and how it was deployed: That Witness could only be Donnie.
Without Donnie identifying that specific piece of paper was passed to him by Jordan during their lunch, its ultimately worthless. Without the tacit co-operation of Donnie, Jordan could deny all knowledge of ever writing/having/passing the note.
The FBI would of course know this to be so. Jordan knows this. Denham knows that Jordan knows this. It's what makes the scene so powerful.
4 No one else could plausibly have gotten hold/known about the post-it
Since we know that the FBI didn't have any surveillance inside Stratton Oakmont (which is why they needed Jordan to go in with a wire), we know they didn't have the building bugged in any way. This isn't because it's not technically possible (We're all living in the post-Prism world, we know what the authorities are permissible of in getting what they want), but because it doesn't make any sense for them to double bluff Jordan like that.
If they had obtained a subpoena and bugged the building, they would have already yielded enough evidence to incriminate all of the Stock Brokers. The fact that they have to vie for it as part of their deal with Jordan indicates it was a valuable asset they were trading off against for a sympathetic/collaborative case with Jordan. They simply wouldn't have pushed for something they didn't need, and wouldn't have been able to authorize such an invasive type of intelligence gathering for no gain: so we can deduce they didn't have the building bugged. Elementary, Watson.
The only people in the room whilst Jordan and Donnie are speaking are themselves, and there is no indication that anyone else is watching/listening nor any reason for them to be.
If there were some secret spy somewhere listening into conversations, Scorcese would either draw our attention directly to their presence (to explain they were being observed) or draw our attention to the fact there is a logic gap in the sequence of events, I.E there is ambiguous information left somewhere, missing. He does neither, choosing instead to draw attention to Donnie: the culprit.
Donnie covers the post it with his napkin, indicating that he understands Jordan.
It is also a way of concealing the post it from Jordan; hiding it is Donnie symbolically saying 'I will deal with this', meaning both the 'problem' presented by the post it note and the post it itself.
Jordan obviously didn't take the note with him, because it ended up with the FBI, meaning he would have had to hand it over to the FBI himself, which makes no sense.
So it's reasonable to assume Donnie was 'left with' the note.
The note was his responsibility, and from that point no one could have plausibly come in contact with it without Donnie's complicit permission.
In summary, there is just far too much evidence and far too many narrative and editorial elements to assume anyone other than Donnie to be the culprit. Scorcese is guiding us to that conclusion directly, and doesn't raise any information that questions the fidelity of this conclusion.