Comment 1 for bug 1426286

It does work, but you need to use absolute paths to any files referenced on the command line. Note also that was never recommended nor supported to run than innermost launcher script directly on the command line (use "/Applications/Inkscape.app/MacOS/Inkscape" or "/Applications/Inkscape.app/Contents/Resources/script" instead - the requirement for absolute paths with the Inkscape 0.91 application bundle to referenced files doesn't change though).

Example:
$ /Applications/Inkscape.app/Contents/Resources/script --file="$(pwd)/rect.svg" --export-eps="$(pwd)/rect.eps"

If that is too inconvenient, I would recommend to install a regular (no bundled) build of Inkscape via MacPorts.

See also my earlier comment in
- Bug #1418650 “Inkscape Shell output path”
  https://bugs.launchpad.net/inkscape/+bug/1418650

Linking as duplicate to
- Bug #181639 “Command-line invocation on Mac OSX partially broken”
  https://bugs.launchpad.net/inkscape/+bug/181639