Interesting enough after nearly 5 years passenger still does not support feature to upgrade Websockets, in this case socket.io.

I have used PM2 to run nodejs app and it requires terminal access, so may not be suitable (and solution) for everyone. I would not call it a solution.

Another way is if hosting company can add proxy pass for websockets in vHost file - this requires terminal acces from their end, restarting apache etc. Again something that isn't end-user friendly.