Yes, Clemenza is talking about Michael's fingerprints. -- 'Hot' and 'cold' are sometimes used by police or criminals. Not as a temperature. If a gun is 'hot,' it means the gun is stolen, or that it has been used in another crime. If it's reported stolen, or it's been used in another crime, there will most likely be evidence left behind which can trace back to the gun. Alternatively, if the gun is cold, it means that it hasn't been used or there's no evidence that can trace back to the gun. In tv shows or movies you might hear the term 'cold case.' A cold case, simply, is a crime where the evidence on record hasn't led to an arrest and there hasn't been any new evidence discovered. So when Clemenza says "it's as cold as they come," he means that there's no way that the gun will be able to be traced back to Michael.
Because of the tape that Clemenza put on the trigger and the butt of the gun, when Michael holds it he won't leave any fingerprints on the gun. Since the tape will prevent any fingerprints from being left on the gun, the gun will be untrackable. Fingerprints can be used by police to connect or track who has used the gun. -- If the gun wasn't cold, the police might be able to track the gun from its' owner to Michael (the owner gave the gun to person A, person A gave the gun to Clemenza, Clemenza gave the gun to Michael, and then Michael would be arrested.)
Anyway, I hope this helps a bit! Sorry if it was a bit confusing.