Running npm install in production server cannot be done in certain scenario (lack of compiling tools, restricted internet access, etc…) and also if you have to deploy the same project on multiple machines, can be a waste of cpu, memory and bandwidth.
You should run npm install --production on a machine with the same libraries and node version of the production server, compress node_modules and deploy on production server. You should also keep the package-lock.json file to pinpoint versions.
This approach allows you also to build/test your code using development packages and then pruning the node_modules before the actual deploy.