We did the Mangrove Nature Cruise last April off Island Princess, but in conjunction with the train ride, not the visit to the Scarlet Macaw Sanctuary. We thoroughly enjoyed the boat tour. It was kind of like the Jungle Cruise at Disneyland, except this was the real deal. We saw many varieties of exotic birds, monkeys, crocodiles and iguanas.
The train ride was very interesting. We saw a lot of the countryside; but we also saw some areas that the Department of Tourism would probably have preferred that we not see.
On a another cruise, we took the tour into San Jose with a visit to Sarchi, although I see those are now two separate tours. Either one is a good way to see Costa Rica's extraordinarily beautiful and varied countryside. The trip to San Jose is long--over 9 hours r/t--but well worth it; and they make ample stops for refreshments and restrooms.