Any obfuscator which is working for Nodejs Express source code
use pkg or nexe module to compile it to binary if you are looking for source code protection.
Obfuscation can easily be reverse-engineered.
OR
Write the business-critical logic using N-API in C/C++ to get compiled node modules.
OR
A paid solution https://jscrambler.com/
If you are interested in Obfuscation,
Refer https://obfuscator.io/ (javascript-obfuscator) , UglifyJS, etc.
Also
https://hackernoon.com/how-to-compile-node-js-code-using-bytenode-11dcba856fa9