You gents picking the Big E, the Missouri, Indianapolis etc aren't looking at this the right way. After the fact, looking back at which ship was the most memorable isn't the same as calling one the pride of the fleet at the time.
I would suggest that going into WW2 within the USN that the USS Lexington or Saratoga were probably the pride of the Navy Aviation guys. As I mentioned earlier the heavy cruiser USS Houston was Roosevelt's "favorite' as he'd used it on a number of occasions.
If I'm reading it right, USS California was the home for the Admiral commanding the Pacific Battle Fleet at the time of Pearl Harbor, which might make her the pride of the battleship navy, although West Virginia, Colorado and Maryland were the last pre-war battleships built.
And for the guy who mentioned the DD USS Johnston, and the DE USS Samual B. Roberts, you can't forget the DD USS Hoel or DD USS Herrmann from that same fight.