In terms of size and several other factors, Yamato and her sister Musashi were great ships...but we also have to remember that certain ships mean certain things to different people.
Without breaking down your criteria into categories, there's several ways to categorize WW2 ships as 'great ships'
Ships that evoked national pride or sorrow:
USS Arizona
HMS Hood
IJN Yamato
DKM Bismarck
Ships with a history of achivement
USS Enterprise CV-6
HMS Warspite
HMS Sheffield
Type VII U-boat (U-99, U-48, U-100, U-47)
Point is, I can name dozens of 'great ships' and find a reason to substantiate it.
Sometimes, it's because of one single event...
USS Missouri (site of the surrender ceremony)
USS Arizona (first major loss of a USN vessel in WW2)
DKM Bismarck (loss of Germany's most famous ship)
IJN Yamato (loss of Japan's most famous ship)
It is, at best, very subjective.
Jeff