There's a pretty big difference between the river habitat and grasslands/marsh/swamp around the Lago

If you drive north on Hwy 35 to Los Chiles the public dock (muelle) is where the majority of Ca o Negro tours start and they're all more or less the same. 10-20 passenger motor launches with canopies that mostly cruise along the R o Fr o rather than going into the official wetlands.
If you turn left 7 km BEFORE Los Chiles and head towards Colonia Puntarenas you'll reach a bridge over the R o Fr o in 7.8 km and then turn left and head 10.8 km south to the village of Ca o Negro where you'll find an assortment of smaller motor boats. The best place to book is the community guide association on the corner of the parque just across from the walkway down to the boat landing.
If you continue 3 km past the village of Cano Negro there's another left turn that takes you 2.5 km down to Bar el Lago which is a good place to launch kayaks if you want to paddle the wetlands on your own.
costaricaguide, three village inn Thanks for the information above, I'll store it away for future use. What are the differences in cost and the differences in the wildlife likely to be seen if using the two boat options?
Before you book, make sure your guide speaks English - some of them don't. We've toured both inside and outside the official wetlands and there wasn't any difference in the wildlife that we saw - great in both places. We've used Sunset Tours, and they're excellent. Desafio is a great company too.
You may find it a little cheaper to go through the guide association but they'll cost roughly the same. The biggest difference is the number of people. From Los Chiles there may be 10-25 others on the boat from Ca o Negro it may be a private tour.
There's a pretty big difference between the river habitat and grasslands/marsh/swamp around the Lagos inside the refuge and therefore differences in the wildlife you'll see but most tours try to give you some of each.