I cannot verify this, but if you cannot identify Aquamacs with system-typeor window-system, then I think you could identify it from the command used to run it. Assuming the executable / link is actually called "aquamacs", then I think something like this should do the trick:
(unless (equal (car command-line-args) "aquamacs")
...)
Otherwise, try M-x apropos-value aquamacs RETsearching for any variables containing this string for use in a similar comparison.
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