Kaepernick was responding to the hip-hop mogul’s partnership with the league.
“It’s all because of her,” the composer, writer and producer said.
Yolanda Adams, Freddie Jackson and Arrested Development will also pick up awards.
Lee spent 32 years with BET before leaving the company last year.
Fox News host vowed to boycott the “pathetic” sports brand.
Regina Hall hosted the show, which saw Tyler Perry and Mary J. Blige receive special awards.
Queen of Hip-Hop Soul delivered a mini-concert.
“Rather than being an icon, I want to be an inspiration.”
Tribute to the late rapper included a star-studded musical performance.
Spike Lee, Ruth E. Carter, 50 Cent, Billy Porter are among the names revealed.