The ex-Marx/K-Line/RMT towers are certainly useable for an American Flyer inspired layout, depending on one's own desires. I've seen photo's of them used to good effect on Flyer layouts. The detail is a little clunky for a scale layout, though.
Fortunately, water and light towers come in all shapes and sizes, so there is almost no "wrong" size.
The Lionel "spheroid" water tower is also usable in S:
As is the HO industrial water tower offered by Athearn a few years ago:
Here's how the two compare:
Rusty