I see a handful of problems here. First of all, in my experience when a witness wants to come forward and take the blame for a crime that has resulted in another's criminal arrest and conviction, no court is going to let him or her do so without an attorney, because he would have to make a knowing waiver of his Fifth Amendment right against self-incrimination. Whoever hears this confession in a court of law is going to first assign him counsel. Counsel will advise him against doing this, because if there is any way the state can still prosecute this person, they surely wiill.
Just applying for a pardon with a notarized letter from a person who can't be cross-examined is likely not going to get you a pardon, assuming, and I don't, that something which is already not a crime can be pardoned at all. It may be better to reopen your case on the matter of newly discovered evidence and have the judge dismiss all of the charges against you altogether. Then, at least, the reliability of the persons' testimony can be verified.
Finally,under CPL §720.35 (1):
“a youthful offender adjudication is not a judgment of conviction for a crime or any other offense, and does not operate as a disqualification of any person so adjudged to hold public office or public employment or to receive any license granted by public authority”.
I understand that you may want to clear your name, but I don't see that going through all this would gain you anything that you don't already have.