In the version of the jslint4java Eclipse plugin that I have (1.0.1.201207042009), there is a field "Exclude files matching these templates from JSLint:" in jslint4java settings; I believe that this is exactly what you are looking for.
This is below the Make JSLint Laxer list on the right; if you have a long list of predefined global variables (like me), you may need to scroll to see it.
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