My preference is for the Sheraton Buganvilias. Not only is it close to the charming town of Puerto Vallarta, but its location right on the ocean and its facilities are quite nice. Plus Vacations by Starwood often have good package deals that often involve bonus Starwood points! If you can, get a Towers upgrade. The butlers and free-flowing champagne are worth the extra charge.
Try http://www.puerto-vallarta.com/index.asp?name=hotels for more info. The Marina and Neuvo Vallarta areas are nice also, but their beaches and location aren't as good as the hotels closer to town. A little too suburban for my tastes.
Regards,
Rick