For those interested, the NFL/NFLPA collective bargaining agreement is available here. Article 46 is the pertinent article.
Section 4 of Article 46 addresses this issue to some extent:
More importantly, in my mind, is the fact that the CBA sets up three or four different types of grievance/arbitration mechanisms depending on the dispute at issue. All of them go to some sort of third party arbitrator or one that is otherwise independent of management, except for grievances of this type. In grievances of this type (i.e., contesting discipline taken for either on field conduct or for "conduct detrimental to the integrity of, or public confidence in, the game of professional football"), the article provides not only that the Commissioner gets to impose the discipline, but further provides that "the Commissioner may serve as hearing officer in any appeal[.]"The Commissioner and a Club will not both discipline a player for the same act or conduct. The Commissioner's disciplinary action will preclude or supersede disciplinary action by any Club for the same act or conduct.
While the NFLPA is arguing that Goodell wasn't impartial, it's going to be hard for the them to win that argument in light of the fact that they contractually agreed that he could both impose discipline and serve as the hearing officer.