We're sailing on the Island Princess March 7.

We usually do our own tours rather than book through the ship but wondering if that's a good idea for Puntarenas-Costa Rica, San Juan del Sur-Nicaragua or Puerto Quetzal-Guatemala.

We like adventure or a really nice beach. What are the best things to do in these ports?

A lot of the people book tours in Costa Rica with Charlie Soto (http://www.okeydokeytours.com/) they had a great time zip lining if that is for you.
We found several tour guides at the dock and would take you where you wanted to go.
There is a beach right at the dock but not sure how clean it is to swim in.
Guatemala we took a taxi tour to Antigua from the port are...there are several taxi's guides there or join a tour from inside the tourist building there ..it was about $45.pp

Costa Rica is so beautiful I'm sure you will enjoy any tour. We took the tour to San Jose, the capital. It was a long ride, but the scenery was well worth it. We booked through Princess. The tour guide was informative and personable--one of the best we've ever had.

More's the pity that Costa Rica, for all it's beauty, has become one of the world's leading destinations for sex tourism, specifically child prostitution, rivaling Thailand and the Philippines - read this link.