If you are planning to catch the public transportation services to Atenas you have 2 departure destinations:
From San Jose downtown: the bus terminal is located in the Coca Cola Market, a well know terminal buses for other routes. The price is about USD$1.62 per person.
From Alajuela town (Airport Area), the bus terminal is located in Terminal Cecosa, just in the heart of Alajuela. Price per person is USD$1.14.