She sang beyond the genius of the sea. (1)
The genius in line 1 isn't Shmoop (though you'd be forgiven for thinking so). Stevens is referring to genius in terms of the spirit associated with place or thing—the spirit of the sea.
Like a body wholly body, flutteringIts empty sleeves (3-4)
"Wholly" sounds just like… holy. Put it next to body and, even though the word and the literal meaning are different, most people are going to think "holy body." Put that together with the fluttering of empty sleeves and we get some pretty clear spirit imagery—almost a ghostly figure. Pretty sneaky stuff there, Wallace, pretty sneaky.
For she was the maker […] for she was the maker. (15-40)
The phrase "the maker" echoes religious references to The Maker, the big guy… you know, God. When we consider that big extended metaphor of "she," the singer, as the artist-poet, we can see the artist as maker and art as religion.