In Chapter 19 of ACOK, Arya
finds Yoren's body in the aftermath of their battle with Ser Amory Lorch and his men.
And she observes how he died:
"The axe blow that had killed him had split his skull apart"
But who killed him?
In Chapter 14 of ACOK, Arya
In the next chapter, they do not find an axe with the Night Watchman's body.
Later on in AFFC Chapter 37, the "hound" is killed:
Notice how this character wielded an axe, and that he is described as "thick and powerful" in this summary:
And consider him and his companions:
There is plenty of motive, evidence, and opportunity to infer this person killed Yoren.