The Stormcloaks are more just in my opinion.
Some Stormcloaks are racist, but that is not what defines the cause. It is freedom, to have the freedom to worship whomever they choose, and to be free to govern their own land.
It's still the Nord's land. They don't own it, but it is significantly tied to their heritage and culture. In my opinion, the Stormcloaks are the Native Americans, and the Imperials are the British Colonists.
The Stormcloak cause is not about the exclusion of other races, it is about freedom. The Imperials are cruel and heartless, and even if the Stormcloaks favor Nords, they aren't genocidal, and they have more close ties to the land of Skyrim.
Thus, I say Stormcloaks.