I have not been, yet... But, really it seems that these are two completely different experiences. I suppose it all depends on what exactly your preferences would be!
Blue Lagoon offers a more 'rustic' atmosphere - from what I can tell. It has gotten very mixed reviews on the boards here in the past. Some really like it, some really do not. Yes, there are hammocks, but I hear that they are set back in the trees, off the beach. Spendid for an adult who wants to relax the day away, perhaps read a good book... But I hear not so convenient for families with children who want to play in the water at the beach... I do not think it is the kind of place with nice beach chairs, etc. No pool. But what Blue Lagoon does offer is the Stingray and Dolphin experiences.
Of course, Atlantis is a very upscale resort type of experience... Casino, Huge pools, landscaping, Beach chairs and service, etc... True, in order really enjoy all of this, the thing to do is to reserve a room at the Atlantis, or the Comfort Suites across the street. And simply take a cab over to Atlantis from the dock. This will give you full access and prividges... pools, slides, beach amenities, entry to tour The Dig, etc... I hear that the excursion is more like their version of a '90 minute time share tour'. And includes a lot of walking (fast walking...) The tours take the ferry over, then you walk up from where the ferry docks to the Atlantis.
We are considering the Atlantis, on our own. It seems to be my preference. Even though it is true that cost-wise, Atlantis can cost quite a bit more.
Hope this helps a little bit. I know I asked this same question when we first started planning our cruise!
Happy planning!