It's easy to set up Code Formatter Preferences for JS file editor but what about Nodeclipse Node.js file Editor?
As of Nodeclipse 0.9 default Editor for .njs files is TextEditor-based. It has no advanced features, except for those in Window -> Preferences -> Editors -> Text Editors
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Right-click .njs file and select Open with -> Nodeclipse JSDT-based Editor
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Then you have all those features found in Preferences under JavaScript (including formatting).
Nodeclipse JSDT-based Editor will be back default for .njs files in Nodeclipse 0.10