Have been to Atlantis twice, once just walking around and then again last July, paying the $25 for the tour and walking around everywhere you're not allowed to go without paying. My advice, pay for the tour! You can get tickets in the casino of the Atlantis. You get to see so much more and The Dig, plus underground acquarium views, is just fantastic. The money seems steep when you're considering it, but I think that the guided tour, plus the parts to the resort you can then explore on your own, make it worth the extra money.
As far as fishing off St. Thomas, try this: go to www.captainnautica.com, check out the excursions, including fishing, and then email them by clicking on the "email captain nautica" spot. The owners of Captain Nautica have become friends of ours through cruising and going on their snorkeling trip; hands down, they are quality people, originally from the USA heartland, and the best company we've ever worked with, even before we became personal friends. If they offer a trip that fits in with your itinerary, you can go with them knowing that you will get the best service and satisfaction guaranteed, possible. I would trust them with anything.