We've been to Puntarenas twice, on Princess, but I imagine the excursions are similar.
I highly recommend the tour into the Capital city, San Jose, with a stop at Sarchi. It is an excellent way to see the beautiful countryside and learn about the country. The tour guides in Costa Rica are excellent.
The other tour we took was a cruise in a small boat in a ecological preserve; it was kind of like the Jungle Cruise at Disneyland, but the real deal. It was combined with a ride on an antique train once used to bring coffee down to the port.