Hi EB,
Getting to Puerto Viejo by bus is relatively easy, we’ve done it before. It’s about a half-day trip. You do have to transfer to another bus in Limon, but buses running south to Cahuita and Puerto Viejo run fairly regularly. To get to Manuel Antonio, you’ll have to go back to San Jose to get a bus going that way, and then it’s about a 4 hour trip from there. This makes for a very long day of travel so you might consider breaking up the trip with an overnight near San Jose. Shuttle vans are another option, but they won’t save you a ton of time for these destinations and are a lot more expensive. The public bus is very affordable- each leg of the trip will cost less than $10. Here’s a website to help you with the bus schedule:
http://www.thebusschedule.com/cr/index.php