This is just what we do....if we have never been to a port before, we generally book tours through the ship. Yes, they are more expensive, but also safer and you know you will be back on board the cruise ship before it sails.
Once we are comfortable with a port, we go out on our own. Part of that is whether a port is safe enough to explore solo. The other factor is, believe it or not, traffic. St. Thomas is certainly safer than a lot of US cities, but can be hard to get anywhere in a timely manner. WHen you do ship's tours, they will hold the ship if need be. Have had this happen.
I am SO jealous that you are going to Isle of Marguarite. I love that place. But, it is one where I would go via ship's tour. I've done Taquantar Village tour twice and would do it again in a hearbeat. Also, Barbados might be one to do a ship's tour.
Another factor is the sheer size of a port. Sometimes, just getting off the ship and walking around a tad is enough. But, you don't really get to see anywhere near as much that way.
I think I've been to all your ports, so ask any questions and I'll tell you what I know and/or think.