The tour with NCL for Atlantis Aquaventure is a 4-hour excursion for $129 that will give you access to most of the resort's facilities including its water park, The Dig, casino, restaurants. I think its a relatively new excursion that NCL Spirit is offering.
I've contacted Comfort Suites myself, and they do still offer passes to Atlantis for any paying guest, although there is a 2-night minimum if you book directly with them. However, if you book elsewhere (say Expedia) for 1-night, they will still give you passes to Atlantis, that is valid for that day till the following day up to 6pm.
Yay! Now I'll look into the water taxi you recommended. I've heard that its cheap, but the trek from where they let you off and Atlantis is a long one.. What do you recall about that? Do you know anything about its land transportation? Thanks!