which one is correct

have not been 是 『現在分詞 Present perfect tense』，其中一個用法是：「現在經常發生的兩個行動，一先一後，先那個用Present perfect tense，後那個用present tense
例：I play after I have done my homework. 我做完功課才玩 (我在說現在的生活情況)
Had not been 是「過去分詞 Past perfect tense」 ,最常用法是：「有兩個行動，在以前發生了，一先一後，先那個用 Past perfect tense，後那個用 past tense」
例：When I was a student, I played after I had done my work. 當我還是學生時，我做完功課才玩 (我回憶以前學生年代的生活情況)
在這段文章，一開始已由 John was a little boy 知道是過去發生的行動，所以 went to spend a holiday是 past tense ,從未到過農場，是更前的行動，用had not been(past perfect tense )才對
另外，the first time in his life that can see such animals ......，我覺得，應該是：
the first time in his life that HE COULD see such animals ......才對

had not been
because it was to emphasis he had not been to a farm before
mostly,
there is a time word"before"
if a sentence have before
we will always use past perfect tense.

以我所以知
had not been 是十分刻意比較 以前兩件事發生的先後

而
have not been 只是說明 從來都未試過的意思

希望幫到你