This page http://tinyurl.com/6tropd5 says San Jose to Manuel Antonio (Directo, 3.5 hours, departs from the main Tracopa bus terminal (Avenida 10, Plaza Viquez), ends in Manuel Antonio. Plus, there are times listed on the page. If you speak Spanish you could probably call
I've taken the DIRECTO public bus from San Jose to Montezuma and it's around $14 and probably a lot longer drive (plus a ferry ride) so I'd guess this is a bit cheaper. The bus has air conditioning with adjustable vents like on an airplane. They check your luggage and give you a claim tag for it. I can't say that this bus is the same way, but it's cheap easy and I'd say it's very safe when I go to Montezuma.
I'll point out that the page above says it's info is from February 2012 and things change. The Montezuma Directo has been from La Coca Cola for many years and they just changed it in the last few months.
This page http://tinyurl.com/cg4juc4 at the same site says it's the comfy Mercedes buses and says $5.
These folks say http://thebusschedule.com/EN/cr/index.php say Transportes Morales runs a directo.
Yes, the information is contradictory. But no one else answered so I'm trying to help :)
I also use these folks http://www.montezumaexpeditions.com/schedules.htm
They do private 10-15 person vans to transport you around and it's more door to door in my experience. But it's more expensive about $45 a person but you'd probably feel safer.
I used to use them all the time, now I just use them when I don't have transport to the bus station (what's the point of the cheap bus if I have to spend $25 on a cab to get to the bus station) or the times just aren't working for me.
http://GarySaid.com/tags/costa-rica/ about 7 years ago