I had the same experience years ago with the Lionel Classics Blue Comet set. These sets seem to have a reputation of having the electronic whistle relay in the tender going bad.
Just replace the whistle relay (either with an old fashioned prewar/postwar one or a modern electronic version) and you should be good.
Replacing it's not the hard part. Bending the tabs that hold the tender body to the frame (and thus chipping some of the paint off) is.
