This is a tough one. I agree that Vertigo is the more complex film, demanding more of its audience, but Psycho broke so many rules and is more audacious in terms of (storytelling and film-making) technique.
Both films have fabulous central performances, great twists...
My opinion might change the next time I watch them, but for now I think I'll have to go with Psycho - you can't hold its legacy against it. That would be like blaming Bram Stoker for the Blade franchise.
(Incidentally, for me, Shadow of a Doubt is Hitchcock's greatest movie.)