johnsuth:
to deal with the destination first ---- not too far from the border, there is a turnoff for san juan del sur. you could get off the bus here and wait for a collectivo or other bus and flag that down to get to san juan del sur. if you want to do this, just tell your driver.
otherwise, go to rivas and take the bus from there.
you can take the public bus from san jose to penas blancas at the border. go through costa rican passport control and walk over to the nicaraguan side, go through nicaragua passport control (there is a small fee - around $10 or less) and then get a bus or taxi or collectivo for rivas or san juan del sur. getting a taxi will be relatively inexpensive and you will get several offers at the border. however, most of the taxis are more or less "piratas" so cars not in the best shape - but they will get you there.
you can take the ticabus, central line, nicabus, transnica or king quality bus -- all international buses with pretty much one or two stops between san jose and the border. air conditioned and with a toilet on board - but more expensive. once again, you can tell your driver to let you off at the intersection for san juan del sur or just get off in rivas.
if you take the international bus and want to get off in rivas, you will have to walk or take a taxi from the panamerican highway to the bus station.
all the international buses have websites. for public bus check here [www.thebusschedule.com]