I live here, so I have been in some of them.
I highly recommend...
Bocabento ...just great.
De Santos ... more for locals, but amazing music and food.
River Cafe ... great location, great food, very romantic.
But, here is a link that will help you to review the Best of 2008 in Vallarta.
Puerto Vallarta, Mexico - Readers' Choice 2008
good luck.
Gina