Indeed, Atomizer is a fine one... I prefer the real drums of Rey Washam (in Rapeman) to the Big Black Tools, but whatever.
Of course, Daydream is excellent, but Bob Bert really turns me on more than Steve Shelley. Therefore, Bad Moon Rising and the attendant EPs really are my preferred SY albums.
I don't have too many favorites, just preferences at this point, but I'm glad to see your list includes more than jazz. For future reference, though, topics like these are usually started in the "Miscellaneous Music" area.