Sure, I'd be willing to make an argument that Way Station was better than Dune. Overall levels of craftsmanship, structure of the novel, plus great aliens and fine characterization. Herbert's novel is a great big untidy heap of interesting ideas.

Better is a useless comparison between unlike things. "More influential" is easy, and Dune wins that hands down. But which is "better", Pound's two-liner about the Métro, or The Cantos?