For babel 6, I used the require hook.
Follow these instructions to get babel register. https://babeljs.io/docs/setup/#babel_register
In your app.js or entrypoint to the application add
require('babel-register')({
sourceMaps: true
});
If you need to add other options as well, see - https://babeljs.io/docs/usage/options/#options
You should be able to use node-inspector & chrome to to debug your application