FYI - The "shuttle" ride from San Jose to MA is quite long - plan on at least 4.5 hours.
Depending on what prices you're getting from Gray Line or other tour companies, it can be cheaper (and much quicker) to fly. I was down there last month (and am going back next week) and flew Sansa from San Jose to MA (and will be doing the same next week).
www.flysansa.com
Nature Air is another option, but their schedule is more limited.
There is a "local" bus from San Jose to Quepos (right next to Manuel Antonio) that is only ~$10 but its non-air conditioned and takes 5+ hours.