A bit late on this, sorry for necro-ing the thread.
I've already commented at length (too long!)
elsewhere on Sgt Pepper so I'll try not to repeat any of that.
It has to be 'Piper at the Gates of Dawn' for me. Whilst all three albums are highly acclaimed, I think 'Piper...' stands apart in that whilst 'S.F. Sorrow' is practically always praised as the pinnacle of the Pretty Things powers, as is 'Sgt Pepper' with the Beatles, 'Piper...' is different in that, as great as it is, it's often overshadowed by later arena juggernauts such as 'Dark Side of the Moon'.
I also think 'Piper...' works better as an album, despite the fact that the other two are meant to be concept albums to varying degrees. There's a continuity that runs through 'Piper...' in both sound and feel that isn't there with the other two. It also has, for me, a sense of whimsy that isn't on even things like 'Lucy in the Sky with Diamonds'.
I generally can't fault 'Piper...' but, for various reasons, and as much as I like the other two, it's easy for me to pick faults with S.F. Sorrow and Sgt Pepper.