I'm running JSLint's Rhino version from the Ubuntu command line like so:
$ rhino jslint.js myScript.js
While the web interface offers various options, I couldn't figure out how to invoke those via the command line. Am I overlooking anything in the documentation?
Yes! You did miss it. You can specify the options for jslint at the top of your .js file. See the doc page and read the options section for an example.