Definitely use number 2. "I am not really into it."

Sentence one is an emphasis on you have no interest in it. Definition b: truly, unquestionably

1. I am really not into it = I am truly not into it.

Sentence two is a statement that you don't know much about it or you don't use it. The definition is "in reality, actually". So "I am not really into it" means "In reality, I am not into it".

https://www.merriam-webster.com/dictionary/really

Use number 2. It will sound more polite.

Sentence 1 is an emphasis on you have no interest in it.  
Definition A: truly, unquestionably

1. "I am really not into it" = I am truly not into it.

Sentence 2 is a statement that you don't know much about it or you don't use it.
Definition B: in reality, actually.

2. "I am not really into it" = In reality, I am not into it.

https://www.merriam-webster.com/dictionary/really