Taps are almost certainly being done by submarines -- there are even books about it[1].
Why would surface ships be around, blatantly giving away what is happening? The likeliest answer is that they screwed up with their anchoring procedures.
My guess would be they create an excuse while elsewhere do it. I don’t picture a boat on top of a submarine performing the procedure. The boat{excuse} is the excuse that renders any monitoring of the signal useless when the tap is done.
Why would surface ships be around, blatantly giving away what is happening? The likeliest answer is that they screwed up with their anchoring procedures.
[1] The best known being Blind Man's Bluff. See also: https://en.wikipedia.org/wiki/Operation_Ivy_Bells