From my understanding, Qt and GTK on the Windows and OS X side are just wrappers around the native GUI libraries, like for OS X it wraps around Cocoa, and for Windows around
There's no clear answer. There's no native GUI on Linux, as there is on Windows and OSX. X11, which is windowing system used on Linux (this applies to Wayland and Mir too), is very basic and low level and is responsible mainly for handling input devices and allocating windows to applications. It does not provide any GUI components such as buttons or text fields. In that sense, both Qt and GTK+ can be seen as "native" Linux GUI libraries. To make matters worse, desktop environment plays a part too. On Gnome, GTK+ can be seen as more "native", whereas on KDE QT is more "native".