Getting into San Jose CitySome of the main bus lines are TransMonteverde, Cóbano, and Tracopa. I got a bus from the Tracopa terminal so I'll use that as my example but most of the main terminals are relatively close to each other.
When you land at SJO, you'll have the usual barrage of taxi drivers and scam artists waiting for you outside trying to sell you a ride. As an example, to get to the Tracopa station, they will start at $30 and make their way down to $20. Uber will cost a bit less (if they're even picking up around the airport as there have been issues with that). BUT just outside the small airport is a public bus stop. And I mean just outside. It's on the other side of the parking structure so you can walk around it on either side.
The walk to the Tracopa terminal was an easy walk and I never felt unsafe (although I've been told that it's not a good area so may avoid it after dark or if you're alone) but I'm surprised my luggage has any wheels left on it at all with the rugged sidewalks and curb-hopping. This was my first experiment bringing a rolly and other than walking around the airport, it has been confirmed why a backpack is so much better. If you GPS map the terminal, the location is accurate. Look for the tall dark blue gated area.
Boom - you've paid a total of $1 to get to your bus station. Congrats budget traveler. :)
Heading West?You don't necessarily have to go all the way into the city to get your bus. This is especially helpful if your flight or bus gets in late and you need to stay overnight the night before. You can stay in Alajuela instead of San Jose.
Buses originating in San Jose and heading West (i.e. to Monteverde on TransMonteverde or to Santa Teresa/Mal Pais/Montezuma on Cóbano) stop at a place called Puente Villa Bonita (Villa Bonita Bridge) in Alajuela that is nothing more than a small covered palapa at the side of the InterAmerican Highway near the road 124 viaduct (they no longer stop at La Radial). There will probably be quite a few people waiting there along with drinks and snacks being sold.
From the airport, you can walk the 3k (25 min) to the bus stop along a thin dirt path. Visit CentroCoasting for photos of the stop. A taxi will run you ₡2,500 ($5) but you might have to haggle since they won't want to make the short trip. Ask them to take you to the parada autobús Puente Villa Bonita.book ahead of time online to make sure you get a seat. They even list Villa Bonita as a departure point. For other bus lines, check to make sure they stop here.
You should be at Villa Bonita around 20 minutes after your bus is scheduled to leave San Jose. The bus might take longer to get there due to traffic but you don't want to risk missing it. Or just take the $1 public bus into the city and start from the terminal of origin.