MRAA - provided by default on the Edison, the MRAA module provides access to the Edison's GPIO pins. Some info here.

Cylon - this is a general purpose 'robotics' module for Node that supports a variety of platforms and outputs (see the website for details). Fairly easy to use with a nice API, great for basic tasks.

Galileo-IO - Created for the Galileo, but also supports the Edison. This is my favourite module for Node development on the Edison as it provides just enough abstraction without providing too much. It also makes things like PWM (a real pain in the arse with MRAA) much easier. Essentially it abstracts reading/writing to the Edison's GPIOs down to an Arduino-style syntax.