I have 2 more of his novels to go, but I think that Omerta is his best work that I have read.
I did like the Last Don, and from what I could watch of the movie, the book was MUCH better.
Obviously The Godfather was a very well done story. The Family was a somewhat different take for him, and though he didn't finish it, it was very interesting in a pseudo-historical manner.
It's been awhile since I've read The 4th K, but that was certainly a different path for him.
Puzo is (was) such a great story teller that most of his novels are good or great. He is probably my favorite writer.