I hate to be the loner, but I think "Super Mario Bros. 3." There's variety, challenge, and good physics. I also love how the music conveys the feel of the sea. Nice color scheme, too. The last 2 items apply to the original "Super Mario Bros." as well.
"World" water levels aren't bad, but they seem samey. I had forgotten "Mario 64" even had water levels, which says something about how enjoyable they are.