My view on this is to book through Atlantis (bahamasdaypass.com). I have not enjoyed doing large group tours through a ship, as you have to wait for the group to gather, be herded to a bus, etc. which eats into time you could be enjoying the destination; plus you are not tied to a specific return time window. Not sure which ship you're doing, but on our recent Dream stop, our time at Nassau was 9:30 - ~ 5:00, so going independently added to time to our Atlantis visit and helped justify the cost. We were down near the front of the disembark line, got to the taxi stand quickly and were enjoying Atlantis in no time. We were there March 1st. Wonderful time!
Note - I believe the one-way cost of the taxi was $4/person, and the only downside was that they tried to gather groups of 10 to fill a van before departure, which isn't much of a deal when there are multiple ships in port; just added a few minutes for the group of 10 to be led to the van, a bit outside the perimeter of the chaotic taxi area.