1) Both "When did you last see each other?" and "When did you see each other last?" are correct.
2)" How long has it been since you haven't seen each other?" "How long has it been since you last saw each other?" Both correct.
3) "How long is it since you last saw each other?" Technically, this is not correct.
Each other ----> I defer to Viviana's comments.
So I am guessing the situation that you are describing is that he saw his family this morning (and now it's the afternoon). But before this morning, he had not seen his family for a while. In this case, we use the pluperfect (past perfect tense) :
"How long had it been since you last saw each other (when you finally met again this morning)?"