If you NPM those modules you can serve them using static redirect.
First install the packages:
npm install jquery
npm install bootstrap
Then on the server.js:
var express = require('express');
var app = express();
// prepare server
app.use('/api', api); // redirect API calls
app.use("https://stackoverflow.com/", express.static(__dirname + '/www')); // redirect root
app.use('/js', express.static(__dirname + '/node_modules/bootstrap/dist/js')); // redirect bootstrap JS
app.use('/js', express.static(__dirname + '/node_modules/jquery/dist')); // redirect JS jQuery
app.use('/css', express.static(__dirname + '/node_modules/bootstrap/dist/css')); // redirect CSS bootstrap
Then, finally, at the .html:
<link rel="stylesheet" href="https://stackoverflow.com/css/bootstrap.min.css">
<script src="/js/jquery.min.js"></script>
<script src="/js/bootstrap.min.js"></script>
I would not serve pages directly from the folder where your server.js file is (which is usually the same as node_modules) as proposed by timetowonder, that way people can access your server.js file.
Of course you can simply download and copy & paste on your folder, but with NPM you can simply update when needed… easier, I think.