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:
- Properties represent the characteristics of a single component or object in the application.
- Options alter global ways that the application works. Microsoft products use this to customise the UI toolbar, for example. There’s an implication here that you can disable UI elements altogether (e.g. a “Simple” user interface or an “Advanced” user interface).
- Settings and Preferences change qualities of how the application works. The implication here is to change, not disable: for example, “Metric measurements” or “British Imperial measurements”.
- Configuration is often where an application is customised for each user or group.
But there’s no single rule.
I’d suggest you use Properties for object characteristics and Settings for everything else that’s application-wide.