If your mother took her 2nd husband’s name, then I would list her with that name. As part of her life story that you may incorporate into her obituary, you can talk about her 60+ year marriage and how he preceded her in death. “She was married for 60 years to John Smith…”
Using “nee” is commonly for stating the maiden name before marriage, but I think you could state it that way since she was married for a such a very long time and that may be the name by which most people knew her.