There are frequent buses going directly from the Coca Cola bus station in San José. Fares are about US$5 each way. If you want to leave from SJO airport directly to Jaco you can use Easy Ride Shuttle Services they run 3 times per day from7to SJO airport to Jaco they also pick up at any hotel in San Jose Downtown or Alajuela Downtown
Alternatively, drive from San Jose past San Ramon toward Puntarenas, until you get to hwy 27. Go south on 27 and follow the signs to Jaco. It's further but much faster since it is not a mountain road. Another plus is that you can stop at the bridge over the Tarcoles River along the way - a prime spot to observe wild crocodiles. Note, it is illegal to feed the crocodiles as they are protected.