xqp (X Query Pointer) is an X.Org utility that prints the ID of the window under the pointer.
xqp [-h|-v] [WID ...]
-h— Print the synopsis to standard output and exit.-v— Print the version to standard output and exit.
If window IDs are given as arguments, xqp won't print anything but will return (via its exit code) whether or not the window under the pointer is in the list of given windows.