If you're heading to the airport, take the short que. Or ask the personnel over there.
The buses between San José and Alajuela are super frequent, but you can feel like everyone knows what's going on but you. There are long lines that people follow to board the bus, but if you ask where they are headed or if they make a particular spot, usually no one can answer. All the bus drivers I have encountered on this bus line are pretty rude.
This is the best bus service to Alajuela and the Airport. If you are going to the Airport do not take the Directo. Take the one that says paradas. Most of the buses are brand-new and very comfortable. The fair is just about $1. You do not need to have exact change.
Buses to Alajuela and the airport is here. The queue is very long.
Saturday is open. Best transfer to airport 1500 colones
From this bus station you can ride to Hard Rock Cafe which is next door (part of) Wyndham San Jose Herradura. You catch the Tuasa bus in San Jose, SJO airport or Alajuela, ie Parada Alajuela. Cost is about $1. Bus leaves about every 15 minutes during the day. Some runs accept large luggage and some don't so if you have large luggage you might wait 30 minutes. From cuidad San Jose, you will have to use overhead crossing walkway to get to Hard Rock cafe.