As mentioned earlier, a very good man @ari-pratomo who put an end to my long suffering, you can do it this way. Take a look at __dirname. If you run your ecosystem.config.js from cli already being at the root of the project - it could help you.

module.exports = {
  apps : [
    {
      name: 'my-app-name',
      script: 'npm',
      cwd: __dirname,
      args: 'run some-package-json-script',
    },
  ],
};