XPLM_API void XPLMBringWindowToFront( XPLMWindowID inWindow);
This routine brings the window to the front of the Z-order for its layer. Windows are brought to the front automatically when they are created. Beyond that, you should make sure you are front before handling mouse clicks.
Note that this only brings your window to the front of its layer (XPLMWindowLayer). Thus, if you have a window in the floating window layer (xplm_WindowLayerFloatingWindows), but there is a modal window (in layer xplm_WindowLayerModal) above you, you would still not be the true frontmost window after calling this. (After all, the window layers are strictly ordered, and no window in a lower layer can ever be above any window in a higher one.)