Hi,
I'm using commander.js for CLI tools. It's pretty straight forward.
A little bit of an effort is needed when you plan to write a CLI for an always running background process which should receive commands from a shell.
In this case, you'll spin up Express.js or Koa.js or raw node-http which will listen on a predefined port for commands. Then you are writing a CLI app which talks via http to that specific port.
Additionally, to commander.js, I suggest some colorings like https://github.com/bucaran/clor