[7] In a game against the Pittsburgh Steelers in 1998, he suffered a neck injury and was placed on injured reserve on December 1, 1998.
[9][10] On August 30, 2004, Boyer was moved to injured reserve which ended his 2004 campaign and subsequently his career.
On February 2, 2016, Boyer was named the special teams coordinator for the New York Jets.
[14][15] In 2021, despite the Jets 4–13 record, Boyer's special teams squad ranked 2nd in the NFL according to DVAO.
After nine years with the Jets, Boyer was named special teams coordinator for the San Francisco 49ers on January 27, 2025.