You could define an absolute path to the binary on a per-project basis, so you could have one default binDir in your CoffeeScript.sublime-settings, then a project-specific binDir in your projectname.sublime-project file. To define project-specific coffeescript settings, add them to a "CoffeeScript" section of the "settings" portion of your .sublime-project file.

For instance, for the project sublime-better-coffeescript, I'd have the following file:

/users/markalfred/repos/sublime-better-coffeescript/project.sublime-project:

{
  "folders":
  [
    {
      "follow_symlinks": true,
      "path": "."
    }
  ],
  "settings":
  {
    "CoffeeScript":
    {
      "binDir": "/users/markalfred/repos/sublime-better-coffeescript/node_modules/.bin"
    }
  }
}

This should override your global binDir for this particular project. Let me know if this works for you

yes, this worked

no, this is still not good enough. it should accept relative paths:

  "settings":
  {
    "CoffeeScript":
    {
      "binDir": "./node_modules/.bin"
    }
  }

because the .sublime-project file is shared among developers and everyone has a different absolute path. and "./node_modules/.bin" doesn't work.