An excellent article from the Harvard Business Review.
They discuss strategies for disagreeing with your boss that range from contracting upfront to disagree (when emotions are at neutral) and then later on, asking for and getting permission to disagree.
Most helpful to me was the nugget taken from the negotiation discipline to discuss intent and shared purpose in the context of a perceived disagreement:
“Discuss intent before content. When the boss gets defensive, it’s for one of two reasons. The first is because she believes your dissent is a threat to her goals. Defenses are far less often provoked by actual content than they are by perceived intent. You can be far more candid about your view if you frame it in the context of a mutual purpose that the boss already cares about. If you fail to do this, the boss may believe your disagreement signals a lack of commitment to her interests.”