I am just starting to learn to use Webpack (previously I just use the manual way to include individual scripts separately). And I used bootstrap-loader for load
bootstrap-loader
Add this as plugin
new webpack.ProvidePlugin({ $: "jquery", jQuery: "jquery" })
and you should be able to have jquery in your whole project.
If issue persists after adding the plugin, try restarting your nodejs server. Remember to install jquery using npm install --save jquery.
nodejs
jquery
npm install --save jquery