LayerBaseSceneView.cs
using UnityEngine;
using UnityEditor;
using System.Collections;
using System.Reflection;
using InternalEditorUtility = UnityEditorInternal.InternalEditorUtility;

public class LayerBaseSceneView : SceneView
{
	[MenuItem("Window/LayerBaseSceneView")]
	public static void Open ()
	{
		ScriptableObject.CreateInstance<LayerBaseSceneView> ().Show ();
	}

	private const int _AllLayerMask = 0xFFFF;
	private MethodInfo _internalOnGUI;
	private int _currentLayerMask;
	private int _selectedLayerMaskIndexies = 0xFFFF;

	public override void OnEnable ()
	{
		base.OnEnable ();
		// SceneView.OnGUIを取得する
		var type = typeof(SceneView);
		_internalOnGUI = type.GetMethod ("OnGUI", BindingFlags.Instance | BindingFlags.NonPublic);
	}

	///
	public virtual void OnGUI ()
	{
		if (_internalOnGUI != null) {
			int visibleLayers = Tools.visibleLayers;
			// SceneViewに映るレイヤーを制限してから
			Tools.visibleLayers = _currentLayerMask;
			// 標準のSceneView.OnGUIを描く
			_internalOnGUI.Invoke (this, null);
			// レイヤーの制限を戻す
			Tools.visibleLayers = visibleLayers;
		}
		// ウィンドウの下の方に、LayerMaskを描く
		Rect pos = position;
		Rect maskRect = new Rect (){ width = pos.width - 20f, height = 20f, x = 0f, y = pos.height - 20f };
		string[] layers = InternalEditorUtility.layers;
		EditorGUI.DrawRect (new Rect (maskRect) {width = pos.width}, Color.black);
		int currentMaskIndexies = EditorGUI.MaskField (maskRect, "Visible Layer", _selectedLayerMaskIndexies, layers);
		if (currentMaskIndexies != _selectedLayerMaskIndexies) {
			_selectedLayerMaskIndexies = currentMaskIndexies;
			_currentLayerMask = 0;
			for (var i = 0; i < layers.Length; ++i) {
				int layerNumber = _selectedLayerMaskIndexies & (1 << i);
				if (layerNumber == 0) {
					continue;
				}
				int mask = LayerMask.NameToLayer (layers [i]);
				_currentLayerMask |= (1 << mask);
			}
		}
	}
}