Sounds like a great trip you have booked. Personally, I have been to Magen's Bay and it is quite beautiful, however, I would definitely recommend taking the ferry over to St. John's and going to Trunk Bay beach. It is truly one of the most beautiful places on the planet and has an awesome underwater snorkeling trail. You can rent the snorkeling equipment right there at the beach for (I think) $5, but don't quote me on the price.
There are several ways to get there, including booking the trip through Royal Caribbean (it is called the St. Johns beach and snorkel tour), or you can simply take the ferry from St. Thomas to St. John's and have more time at the beach. It really is not difficult to get there.
Either way, good luck and have a wonderful vacation.