If you are looking for another destination between Manuel Antonio and San Jose, Jaco might be good. It’s a popular beach town with tons of stuff to do. We wrote a post all about it (Jaco: Costa Rica’s Booming Beach Town) which includes some hotel, activity, and restaurant recommendations. We included a couple hotels a bit outside town if you don’t want to be right in the tourist mix. If you are looking for a more natural setting you could also check out the town of Tarcoles, which is a much smaller fishing village just north of Jaco. This area is famous for Carara National Park and the Tarcoles River, which is great for seeing birds and gigant crocodiles. A couple of hotel ideas near Tarcoles are: The Macaw Lodge, Villa Lapas Rainforest Eco-Resort, and DoceLunas. Hope that helps give you some ideas!
Answer for suggestion for place to stay between Manuel Antonio and San Jose