You should be aware that the tour of San Jose involves two hours each way on a bus on narrow, winding mountain roads just to get there -- and that's if you don't hit traffic.
The people who went on the ecotours did seem to enjoy them, though they also reported that the bus rides were rather long and tedious.
I agree completely about Wes's comments about Sarchi, having just been there. The metal church that you will visit on the same tour also is a true work of art, and definitely worth seeing. Even on this tour, though, the bus ride (one hour each way) is somewhat tedious.
Puntarenas has a brand new cruise ship pier where the ship will moor upon arrival. It's really easy to wander into the historic fishing village of Puntarenas, which has not yet developed into a tourist trap, to shop for local items.
In Cartagena, all of the shore excursions are pretty similar. The major difference appears to be that one gets out to visit the fort (at the expense of some shopping time -- which was more than sufficient anyway), the second drives past the fort without getting out to tour it, and the third skips the fort completely in favor of more shopping time. Your choice.
BTW, you might want to check my post in the "sun princess excursions" threat on this message board for comments on the other ports of call.
Do have a great trip!