I would do (and did) the all day bus tour in Panama. Here is why. Are you going back?
If no then you will want to see as much as possible and this is the way.
You will go across the isthmus to Panama City. There you will see the ruins of colonial Panama City, the Old City , the new modern city. You will stop at the Church of the golden alter, the opera house, and Balboa monument. Lunch is at a restaurant in the former Canal Zone and before or after you go to an area containing local souvenir stands (also in the former canal zone). You stop for a tour of Mira Flores locks and most of the time get to see a ship or two going through,. You get to see it right up close and it is facinating. The tour is long, but you see a whole lot of the new and old country and the canal. More on this tour than any other.
In Costa Rica if you want to see the natural countryside and all of that go on the Torteguero Canal tour. You will see plants, flowers, trees, cranes , flamingos, herons, turkey vultures, monkeys, sloths, goats , and the highlight will be crocadiles , lots of crocadiles. Scenery beautiful, boats and buses and tour guides are first class.
Have a nice time.