There are a range of excursions to the Marietas. There are one or two tour companies that have big catamarans. There are also a few companies in the small village out the back gate of Punta Mita that will rent a panga with guide for about $300 for three hours (price can be negotiable). We have hired a panga with guide several times (we have a house in Punta Mita) and it is always a great trip. Some guides are better than others - it's luck of the draw, really.
St Regis partners with Punta Mita Expeditions, whom we have used several times before. We have always had good experiences with them. They have a web site with a lot of information on their different packages.