My brother used to live in Venezuela (Caracas) for several years, and they enjoyed spending some of their vacations on Isla Margarita. Like all tourist areas and 3rd-world countries, a little street smarts are a good idea (such as leaving your jewelry onboard ship, drinking only bottled water and avoiding drinks with ice in them, being aware of your surroundings, etc.) However, I don't think you need to be unduly frightened of this port call.
On any cruise, I usually use a hip pack with secure belt (the kind with a metal cable in it, so it's hard for a pickpocket to quickly slice & grab it) and I carry only what ID is required, plus maybe $20-30 if I plan on shopping. (You can tell I don't buy big-ticket items!
) Carrying a copy of the first page of your passport is always a good idea in a foreign country.
I do recommend taking a ship's shore excursion if your cruise calls at La Guaira (Caracas), and if you are at all nervous about Isla Margarita, then stay with a ship's shore excursion there as well. Wherever you end up going, enjoy!