America Travel operates the Tico Tren which runs every weekend from San Jose's Pacific Railroad Station to Mata De Limon, near Puntarenas. There on transfers to an airconditioned charter bus for the short ride into town.
The trip traverses the central valley then ascends through mountain passes and tunnels. Encountering the fertile regions on the other side of the mountains, the train passes through beautiful farm lands and orchards. Don't miss buying fresh fruit when the train stops at Orotina.
A friendly crew serves coffee while vendors sell sandwiches as they walk through the railroad cars. It's cheap too; only $25.00 round trip.
The public bus station is just one block ahead from the cruise dock, (East) but you should know the service is very poor, there is a big station with blue/white buses but this is service to San Jose, buses to M.A. are leaving every 3 hours and they just stop to pick up at the road side, if you are planning to get this transportation back and forth for one day (10 hours) as mostly of the cruise ships are schedule to call on this port, I don't recommend you this choice, the bus take about 3:30 hours to do this trip one way, it is so tight and you'll be most of your time on the bus, if you drive it takes just 2 hours but there is no reliable rental around Puntarenas, there is thrifty but not well managed. I recommend hiring a driver for the day if you don't want to get a ship's excursion.
Odyssey Tours CR is highly recommended on many forum sites.
We leased a car at the airport and drove all around the country side.
The roads are full of potholes so it may take longer to get where you are going but you will get there.
Sometimes there are no road signs when you come to a 4 way stop so you just guess.
Just buy a good map and hope.
There are two ferries that leave from Puntarenas.
One is a car ferry and one is for foot/bike passengers only.
We took the car ferry to Playa Naranjo, on the Peninsula Nicoya west of Puntarenas.
It took us 1 1/2 hours to cross the Gulf of Nicoya.
Tours to and around Puntarenas and all Costa Rica. Air Condition, Full english spoken, private chauffer.
this shortcut will save you time getting between Nicoya and the mainland, but arrive early, you may have to wait a while!