So this scanner is attached to a client computer where the web app runs in a browser? If so, you'll need some native code for the web page to interact with the device, and that code needs to break out of the browser sandbox - possible ways to do that would be Java applets (obsolete and not recommended), Flash (also on its way out) or Microsoft technologies like ActiveX or Silverlight that limit you to IE/Edge on Windows. Browser plugins may also be a way to to this.
I recommend to consult the documentation of the device to see what they have to say about interfacing with it; there should be code examples as well.
Web services do not sound like the right approach for this.