Option No. 4: Marquand Manuel (Jets safeties coach)
Kyle Shanahan might not want a castoff coach like Mike Pettine, instead opting to go with an up-and-coming figure to lead the defense.
One candidate who'd potentially be perfect is current Jets safeties coach Marquand Manuel.
A former pro safety who was on the Seattle Seahawks' Super Bowl-winning team from 2013, Manuel has plenty of coaching experience in the Cover 3 zone-style defense the Niners have mostly employed since 2017. Manuel was also there with Shanahan with the Atlanta Falcons in 2015 and 2016, too, as an assistant.
As for the present, Manuel is serving on Robert Saleh's staff, which would help with schematic continuity if he was targeted by the Niners.