I've been over to Blue Lagoon several times. It is one of my favorite shore excursions off Nassau. They have really fixed it up and improved it since it was devastated by a storm. The staff is wonderful, and you've already read my Cheeseburger comment.
If you don't want to do the Dolphin Encounter through the ship, you can book directly with them for just the beach and lagoon. Just take a taxi over the bridge to the ferry terminal. I think the taxi is $4.
The ticket office is located in the terminal and they'll give you a wristband that says what package you are on. Mine always says Blue Lagoon Beach Day. If you booked for lunch included they'll give you a ticket. I always do because the Cheeseburgers are truly wonderful. I started going back in '93 when it was called Gilligan's Island. It's real name is Salt Cay.
The return ferry runs every other hour I believe, and taxis or sometimes a bus are available to take you back to the cruise ship terminal from the Paradise Island ferry terminal.