There are several words with similar (in some sense) meaning:
Options, Settings, Properties, Configuration, Preferences
English is n
Tricky, this, as there's no one single consistent style followed by all applications. As you say they are (broadly) synonyms.
In truth it doesn't really matter so long as your expected audience understands what you mean.
The biggest difference is between Properties, which usually affect a component or object, and the others, which affect the whole application.
Following an approximate lead from Visual Studio and other Microsoft products:
But there's no single rule.
I'd suggest you use Properties for object characteristics and Settings for everything else that's application-wide.