The bus stations are at the beginning of the peninsula on the right side of the map below. I come in from San Ramon at the station closest to the water. I think that is where the San Jose bus comes in too. The station a little further north has the local routes listed above.
The ferry is located at the left end of the peninsula on the map below.
Note, Puntarenas can be a good station to get further down the the coast to places like Jaco