Well, the excursion to San Jose is really much more than just a "bus ride"; it's a good chance to see the beautiful vistas that are Costa Rica. And you make some very interesting stops along the way. A good tour guide (and we have only had great ones in Costa Rica) makes it a very informative and educational experience.
Puntarenas is just a very poor and not-too-clean port town. I wouldn't venture more than a few blocks from the pier.