I've just completed a one-week natural history cruise as a lecturer aboard the Sea Voyager, operated by Lindblad Expeditions/National Geographic Expeditions . What a trip!
I'm often asked how to get to remote areas of Costa Rica that few visitors ever see. Well, getting there by sea is one answer.
Three companies currently operate natural-history focused cruises that put you ashore at relatively off-the-beaten-track locales up and down the Pacific coast. Typically, you'll cruise at night so that each morning you're already anchored at a new location, when you'll go ashore by Zodiac to hike trails in the company of naturalist guides. I'll guarantee you'll get to see lots of monkeys, macaws, and who knows what other wildlife. We even saw pilot whales and blue-footed boobies on my recent voyage. There's usually plenty of time for snorkeling, even horseback rides, and cultural encounters too.
The 64-passenger Sea Voyager operates 8-day trips that combine Costa Rica with Panama, including a crossing of the Panama Canal. These trips appeal particularly to birders and nature lovers. Highlights of my recent trip included hikes in the remote San Pedrillo section of Corcovado National Park, a visit to the Orchid Botanical Garden (in the Golfo Dulce, and accessible solely by boat), and the requisite full-day of activities at Manuel Antonio National Park; plus stops at seabird nesting sanctuaries off the Panama coast, and snorkeling and hiking at Isla Coiba National Park. At night, lectures and/or video/slide presentations enhance the learning experience.
Cruise West  operates similar trips from Los Sueños Marina aboard the 100-passenger Pacific Explorer, with similar stops as the Sea Voyager.
If you're seeking a less nature-focused, more up-end experience, consider Windstar Cruises , which sails out of Puerto Caldera and anchors at Drake Bay, Quepos, Playas del Coco, Isla Tortuga, and San Juan del Sur (in Nicaragua).
I shall be lecturing (on Panama and how to improve your travel photography) aboard two special National Geographic Expeditions cruise-tours in October and November. Why not join me?