The primary difference in the use of magic in both Shoeless Joe and Harry Potter is the difference in genres. Harry Potter uses magic in a fantasy manner. Its use of magic is created in a separate reality, one that is evidently not part of this world. Hogwarts Academy, for example, is not meant to be a component of current existence. Harry's use of magic is not understood amongst "regular people," and this is why the use of magic is in an alternate or separate state of being. Again, it should be noted that in this setting, Harry is in control of magic, and he is the agent that can utilize it and understand it in his quest to battle the evil forces such as Voldemort.
In Shoeless Joe, the magic that is displayed is part of a magical realism. This magic happens in reality, Ray's reality. It is a world that is not separate, but actually a part of the reality that confronts everyone. Ray has bills that need to be paid, in laws he doesn't particular enjoy, and has tried other jobs and failed at them. Ray is not endowed with any special powers and does not really control the magic that is present. It takes him by surprise, as he seeks to understand "the voices" and their cryptic messages such as "If you build it, he will come" or "Ease his pain." Ray is not the agent of the voices, nor does he understand what is meant by them. He is not a sorcerer who can "create" magic, as it rather simply happens as part of his reality. There is little to suggest in the novel that he knew Shoeless Joe and the Banished White Sox players would arrive upon building his field. There is little that purely indicates to him that Salinger is to be brought to this field, and even less to indicate that Ray's reestablishment of bonds with father and brother will be the result of his quest. Ray's "magic" is more of a consequence of his actions, and not of direct intent. In this setting, magic is part of the world around him. Whereas in Harry Potter, the magic used is that of wizardry, in Shoeless Joe, the magic is within the reality of the character and is more reflective of his emotional development.