Command line settings are available to your app, but only on the server. In client code, process.env doesn't have them. You can write a Meteor method, so that the client can ask for environment settings. There are potential security risks with this approach because you are allowing access to server settings on the client and potentially revealing them to the user.
You could put settings in a database collection, and your code will read them from there. That's probably a better way, as each deployment can easily have different settings.
If you want to use process.env, you can either do it on the command line,
MY_ENV=xxx meteor --port 3010
Or you can put them in a shell script like this
#!/bin/bash
export MY_ENV=xxx
export MY_ENV2=yyy
meteor --port 3010