Allowed EOLConversion to change Editor Settings.

The editor setting isn't documented, but it is available and editable.
Wasnt able to determine when it was added but it does work for Unity 2018.1

Author: Lachee

Editor/Tools/EOLConversion.cs

@@ -17,6 +17,9 @@ public class EOLConversion : UnityEditor.AssetModificationProcessor
         private static void ConvertToWindows()
         {
             EditorPrefs.SetString(PREFS_PREFERED, "\r\n");
+#if UNITY_2018_1_OR_NEWER
+            EditorSettings.lineEndingsForNewScripts = LineEndingsMode.Windows;
+#endif
             Convert("\r\n");
         }
 
@@ -25,6 +28,9 @@ private static void ConvertToWindows()
         private static void ConvertToUnix()
         {
             EditorPrefs.SetString(PREFS_PREFERED, "\n");
+#if UNITY_2018_1_OR_NEWER
+            EditorSettings.lineEndingsForNewScripts = LineEndingsMode.Unix;
+#endif
             Convert("\n");
         }
 

package.json

@@ -1,6 +1,6 @@
 {
   "name": "com.lachee.utilities",
-  "version": "1.4.6",
+  "version": "1.4.7",
   "displayName": "Lachee's Utilities",
   "description": "Bunch of utility functionality",
   "unity": "2019.1",