Is 5S Methodology shall requirement of IATF 16949?

5S is not a requirement of the IATF 16949: 2016 standard. 5S is a customer-specific requirement from Toyota. If TOYOTA is your customer, you have to comply with 5S requirements. 

However, in the article 7.1.4.1 of the IATF standard, "The organization will maintain its facilities in case of an order compatible with the product and production process needs, in case of cleaning and repair".  Even if it is not specified as 5S in the IATF 16949:2016 standard; nevertheless, cleanliness, order, standardization is a very important issue for automotive expectations.

These issues, as you know, are the main foundations of 5S and must be complied with as an IATF 16949:2016 standard requirement.