There is no "day tour" center with a roster of excursions and set prices; instead, you'll need to hire a local boatman and negotiate a price. If you're staying on the island, your hotel can organize a boat tour for you with a local, or in a pinch you can find a boat and driver at the main dock near Cabañas Jackson, or at the pier in La Guaira. It's best to plan ahead and reserve a time with a local boat, but on slow days you shouldn't have a problem finding a willing captain. Also, check the pier at the Hotel Isla Grande, or check with the staff there to see if they have boat trips planned.
Day boat tours usually include a zip through a mangrove swamp and a visit to one of the offshore islands such as Mamey Island, a private island up for sale but still open to day visitors. There is a fine white-sand beach here with good snorkeling opportunities, but you'll need to bring your own gear. This trip can range between $35 and $50, depending on the amount of time you'd like to stay on the beach (in the event that they drop you off and pick you up later).