I was in Playas del Coco about four weeks ago for my sons open water dives and the trip was about 5 hours but we stopped for lunch so it should be about 4 hours non-stop. Bear in mind than there is a new traffic law going into effect in September after which if you are caught speeding is a big deal, and in Costa Rica speeding is anything above 50MPH and at that speed it will take more than 4 hours.
Playas del Coco is Ok I guess, the popular places to dive there are Punta Gorda, Play Penn (where there is a small, very small, sunken fishing boat), Monkey Head, Punta Argentina, and such; but if you dont mind my suggestion, why dont you go to Flamingo and dive in the Catalina Islands?
I took my son last week for his first graduated dives and the place is awesome. The hotel rate was $99 for a pool side room at Flamingo Beach Resort. We used Acuacenter as the diving operator and they are very professional and they know the area. Ive been using them since 2003 when I started diving and have never had a problem. They can even put together some hotel/diving packages. The owners name is Eduardo and he is an OK guy.
Finally, I would suggest you fly directly to Liberia, rent a car there and drive to Flamingo, why would anyone go to San Jose anyway?! Flamingo is about a 90 minute drive from the Airport in Liberia and they have signs all the way in. Flamingo itself is kind of dead but you have Tamarindo 15 minutes drive away and that is definitely not dead. Even if you go to Playas del Coco, you should fly to Liberia and not to San Jose, unless you have to come here to the city.
Here are the links of the places we were last week if you are interested:
Aquacenter Diving Costa Rica, Scuba Diving and Adventure Tours in Costa Rica
Costa Rica Hotels, Beach Resorts & Beachfront Room Reservations - Flamingo Beach Resort
Finaly some pictures we took last week at Catalina Islands:
Good luck