Entering this nengo --port 9999 into a new Terminal window seems to create a new (and separate) Nengo server within which a separate window can be opened.
I can confirm that if you want to run multiple NengoGUI instances, you’ll need to create each one with a separate port number. NengoGUI runs using a webserver and a browser. Separate Nengo instances need separate web servers, and each need their own port so that they don’t clash with each other.