Cruise ship tours are nothing more than local tours under contract to the cruise line. So yes, you pay double for usually less than half the trip you can arrange on your own.
Do your research, use a reputable company, and you will be at least as fine as with the cruise ship tours. You may even occasionally be ON the same tour.
I did Eli's Eco tour in Antigua and without a doubt, it is in my top 10, probably top 5 shore excursions, anywhere, period. Not available through any cruise line...