Hi, a friend of mine would like to travel to San Jose, Costa Rica from Cape Town, SA, by boat. I have researched for him: freighters, passenger cruises, small boats, etc. I am unable to find any info. Does anyone know how to go about this?

San Jose is inland! You can get a cruise ship to Rio from Cape Town but I doubt you'd find anything going further north.
If you wanted to be a crew member then you'd need skills and experience. Freighters - I guess it would depend on their insurance issues?
Try posting in the Life on the Ocean Wave branch

If you are in cape town, go to the Yacht Club, they have notices on the board, loads of people looking for crew.
Freighters follow freight lines, just as trains.
I strongly suspect there isn't a line doing both places.
A yacht might be the better option, but then, it's quite obscure nevertheless.
An interesting question to which I certainly do not have an answer. However, there must be yachts sailing from Cape Town for the Caribbean and if you follow #2's advice you may just be able to join as a crew member. Of course, getting from the Caribbean to any of the Central American countries may be a second problem. You could fly from many of the Caribbean islands to Miami and then on to San Jose or Panama City.