So you're in Puntarenas today in Costa Rica, the best tour would be the train and boat tour on the
Tocarles river to look at the giant crocodiles in the wild. Or walk around the local craft market right off the ship and have a beer in the German restaurant which sits on a corner one block away.
Macapa is just a stop for pilot pick up, lots of pickpocket problems there, watch out. The 2 you don't want to miss are Boca de Valeria and Parintins, and I don't think you're stopping there but Alter de Chao is a beauty and safe.