It appears that Joan Lee was 95 at her passing.
The first link that you provide is to The Hollywood Reporter. In the report, they include this correction on the bottom.
July 7, 4:40 a.m. An earlier version of this story incorrectly stated Joan Lee was 93. She was 95. THR regrets the error.
This can be validated by finding an article from The Chronicle entitled Comic book legend Stan Lee inspired by Newcastle-born wife. In the article, they mention
Joan, now 90 and still living with Stan in Beverley Hills, California, has told the Sunday Sun of her fond memories of life in Newcastle.
This article was published October 23rd, 2011, implying that Mrs. Lee was 90 in late 2011. If she was, she would had to have be either 95 or 96 at the time of her passing in July 2017. There doesn't seem to be a source on her actual birthday, with Wikipedia only listing it as 1921. However, this fact seems to have been recently added, and it appears that Wikipedia itself had the fact wrong for an unknown amount of time.
It seems like this may be a case of Citogenesis, where Wikipedia had incorrect information that was then used by news reports and then validated by those same news reports.