In Eclipse, got to Run > External Tools > External Tool Configurations
Double click on Program to open a new configuration and name your new configuration (ex. Node_Config)
Figure out where you have node.js installed. Paste the results in the 'Location' box in Eclipse. (If you haven't installed node, do so here)
where node, or see this for more/different windows advice
Fill in the following:
Click apply, and then close.
Now, in the main Eclipse screen, find the play button with a red toolbox (next to the regular play button). When you have a js file open that you want to run, click this and it will be just like running it from your console using node.