ソースコード

using UnityEditor;
using UnityEngine;

[InitializeOnLoad]
public static class Example
{
    static Example()
    {
        EditorApplication.update += Update;
    }

    private static void Update()
    {
        var mouseOverWindow = EditorWindow.mouseOverWindow;
        var sceneViews      = SceneView.sceneViews;
        var isOver          = mouseOverWindow != null && sceneViews.Contains( mouseOverWindow );

        Debug.Log( isOver );
    }
}