US Naval Observatory has assigned sunset times per time zone. Should
these times be used for navigation of inland waters or should the
sunset times pertaining to a particular zip code be used or the sunset
time printed in the local paper because the all can be diffrent.

I cannot understand how anyone can navigate inland waterways with
reference to times of sunrise or sunset, but as you point out, the
Naval Observatory times - one for each time zone -  could only be of
minimal help, since within each time zone the actual local sunrise,
-set times will vary by about one hour.