From your config file, it seems like you're only excluding node_modules from being parsed with babel-loader, but not from being bundled.
In order to exclude node_modules and native node libraries from bundling, you need to:
target: 'node' to your webpack.config.js. This will exclude native node modules (path, fs, etc.) from being bundled.node_modules.So your result config file should look like:
var nodeExternals = require('webpack-node-externals');
...
module.exports = {
...
target: 'node', // in order to ignore built-in modules like path, fs, etc.
externals: [nodeExternals()], // in order to ignore all modules in node_modules folder
...
};