Technically no.1 is correct out of those two. But normally we would say that sentence as "I never would have thought he would leave me before yesterday".

#1 is correct. 1. I had never thought he would leave me before yesterday. I had never thought << == [past perfect for a state or action earlier than "yesterday"] he would leave me <<== ["would leave" is the future-in-the-past form of "will leave" ] before yesterday.

Я не могу поверить ,что он бросил меня прошлой ночью.