It is still a myth as far as our modern civilization is concerned, Atlantis located somewhere within the devil's triangle and it's inhabitants had struck down many planes and vessels daring to disturb the peace. Without resorting to magic how can Atlantis disappear from the sonar? (Answer with most primitive tech wins.)
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When Atlantis was sinking, the residents knew about it only slightly in advance. Being sensible people, they rushed into their basements and shut the doors. One atlantis had sunk, they dug between the basements to form a network of underwater/underground rooms. They somehow figured out how to get air down there (and how to build airlocks), and decided there was no reason for them to move. Over the past thousand years, the sea gradually destroyed all of the buildings.

If you know what to look for the doors aren't hard to find, but the lack of above-sea-floor structures make it almost impossible to locate on sonar.
If the Atlanteans wanted to be invisible to radar they could use materials similar to the rubber like tiles used on submarines. If they needed a particularly primitive version of this then large amounts of organic matter, especially seaweed of the sort with the flotation air sacs, would be useful in deflecting and absorbing sonar if strung out above their city.