Hi Yoga Mama, 
Yes those are great places to see while you travel Costa Rica for three months. Each has a completely different feel and landscape. You can easily spend several weeks in each place and make shorter trips to surrounding communities and attractions. One exception might be Monteverde since it is remote and there are less things around. You can probably limit your time in Monteverde to a week or two and still experience most of the sights there. A couple other places you might want to consider, which are popular yoga destinations, are Nosara, Montezuma, and Dominical.

 
As for getting around, yes Interbus is very comfortable, they are a shared shuttle van service which takes you from hotel to hotel. The prices vary depending on the distance but most trips are around $30-$60 per person. Children under 12 years old will be half price. Note: to get between La Fortuna and Monteverde, the best route is a shuttle/boat combination commonly called the jeep-boat-jeep. You can book that locally once you arrive but it is a big time saver.