Our Top 10 Costa Rica Itineraries book has a chapter on the Best of Costa Rica that would be helpful for planning your time in Quepos/Manuel Antonio. It has ideas for good beaches, hikes, and day trips. Another good resource is our blog on 7 Off-the-Beaten Path Things to Do Near Manuel Antonio. Since you’ll have a car you might also want to look at our post on the Nauyaca Waterfalls, a little south near Dominical. That’s a nice hike to a gorgeous waterfall.
Answer for Suggestions on an itinerary for 4 whole days in Quepos?