Hi Tomi,
You are not asking for something that is easy.
First,
Try opening a reference to the VI in question and use a property node to get the "FP.IsFrontmost" property. This boolean will tell if the Front Panel is on top of the pile.
I AM NOT SURE if that will be false if there is another (non-LV) application on top.
If the boolean does not reflect this state,...
Then you will have to use the functions in "WINUTIL.LLB" (search for lvwutil32.zip) to get the state, bounds, and position of all of the windows and do the math to determine if there is an overlap. If you want to just for an over lap of the graph, the math get a bit more complicated.
I did mention that this was not going to be easy didn't I?
Trying to help,
Ben