If the window hasn't been created by JOGL even though JOGL "knows" its OpenGL external context, there is no mean of obtaining its mouse events. There is nothing magic, JOGL is able to manage only the events of the windows it creates that it passes to its listener. Maybe you can wrap the window created by your native C++ code into a proxy surface by using
this method, see how it is used in our SWT canvas, you'll have a chance to get the mouse events. You have to find how to use this proxy surface to create a NEWT window and then you'll be able to add a mouse listener into it.
I plan to implement a new input API for NEWT but only focused NEWT windows will be managed.