I haven't seen all of his, but I think the shining is my favourite. So much intricate design. Didn't think much to a clockwork orange. Eyes wide shut was very good though, as were 2001 and full metal jacket.
I'd argue for Barry Lyndon personally, but it's pretty good. It's not better than 2001 or Paths of Glory or anything, but I think it's better than people give ('gave'? I'm not sure where everyone's at with the constant reappraisal of his initially lesser-liked films) it credit for, and unmistakeably Kubrick.
I love Kubrick and there's a lot to admire about EWS but it is definitely not his best. It looks great as you would expect from Kubrick, but is also turgid and overlong. How can an orgy be that boring ?
Also not helped by the casting. Kidman is annoying in a pretty minor role tbh, and Cruise is unintentionally hilarious. Btw is his character's habit of simply repeating the dialogue of the person he's speaking to intended as some kind of joke!? He was great in Magnolia though, from around the same period.