Any number of scenes could provide a variety of answers to your question, but I'll offer one.
Junior's first day at Reardon is certainly an important event and transformation in the novel. In this scene, all of the apprehensions and anxieties of crossing the divide from one culture to another come to fruition. Junior is initially ignored by the white students but the taunting and threatening remarks soon follow. Of course, these tensions continue to boil within Junior an eventually he is driven to violence is retaliation.
So much of this novel is about living caught between two radically different worlds. This scene when those tensions become a physical reality is certainly one of the novel's most important.
I agree that there are many great scenes in the novel. I think the most important scene is at the end of the novel when Rowdy and Junior have become friends again. One of the major conflicts that Junior faces--in addition to his difference from those at Reardan--is the conflict and pressure that he feels from those on his reservation after he decides to leave to attend school in another place. Junior is seen as a bit of a "sell-out" after he makes this decision, and he is immediately alienated from his own community. This is incredibly difficult for Junior to deal with, so when he and Rowdy become friends again, a significant resolution is reached. Junior sees the beauty that the reservation has to offer, and Rowdy understands why Junior decided to aim for what he saw as a better opportunity.