They can be found in more than one place:
~/Library/Preferences/com.example.myapp.plist
~/Library/SyncedPreferences/com.example.myapp.plist
and if sandboxed
~/Library/Containers/com.example.myapp/Data/Library/Preferences/com.example.myapp.plist
~/Library/Containers/com.example.myapp/Data/Library/SyncedPreferences/com.example.myapp.plist