One level of comparison is that both take an insider's look at a moment in history and tell it as a narrative yet intentionally superimpose commentary over the narrative. What this means is that the narration and form--graphic novel (comic book)--illustrates a perspective on and an interpretation of events that stands apart from events. In Footnote, this is through the journalist's voice:
They could file last month's story today--or last year's, for that matter--and who'd know the difference?
This may be further illustrated briefly through the characterizations in Maus being developed as cats and mice and pigs (cats: Nazis; mice: Jews; pigs, Polish).
A level of contrast is that while Sacco was able to immerse himself in the living history of Rafah to find the hidden history of one overlooked event in 1956, Spiegelman had no way to accomplish a similar feat. The Shoah (accepted Biblical term meaning "calamity" that stands for the Holocaust) happened once in history and cannot be re-entered--as life in Rafah might be entered--as survivors were dispersed and incidents are unrepeatable. Yet, Spiegelman does immerse himself in life, beginning before Hitler, by telling the story of Pop's life to his son.
But this what I just told you--about Lucia and so--I don't want you should write this in your book. ... It has nothing to do with Hitler, with the Holocaust.