In short, option 2 is your answer.
The following is an explanation of preparatory "it".
Imagine that, A has help B solve a problem. B appreciates that.
A: I am willing to help you, call me anytime.
B: It's nice of you to say so!
replace "so" with "that"
B: It's nice of you to say that!
"that" here refers to what A just said, which is a standard use
used to refer to something that has been mentioned or was involved earlier
"that" = "something was involved earlier" = what A just said = "I am willing to help you, call me anytime." = the content A said
"it" refers to the action/behavior of saying that
"It's nice of you to say that" = "saying that" is nice of you.
"that" = the content A said
"it" = "saying that"
with option 1, "that" refers to two different meanings at the same time, which should be avoided.