The choice is dependent upon many factors including the size of your group and the size of your budget and, for our family of four, we find that a blend of the two works best.
Some ships dock in ports that are well located and easy to get around. Others, not so much.
Some cruise ship excursions add benefits that are hard to obtain on your own and others are simple to replicate.
For a complete look at the pros and cons of planning your cruise ports of call, I wrote a page that explores the benefits of cruise ship excursions versus doing it on your own, which you can read by clicking here. My hope is that my page will not make the decisions for you but that it will help you think about the issues as they apply to your personal situation.
Ports of Call: Cruise Ship Excursions Versus Your Own Excursions.
Order your copy of Frommer's Cruises and Ports of Call from Amazon.