I'm working on a manga called "Nightfall Academy" and I'm trying to translate the title to Japanese. But, since I'm still studying the language, I'm not sure which term is correct. Should it be (日暮れ) Higure or 薄暮 (Hakubo)?
First of all, do you have a good reason to write this in all-katakana? It's sometimes a reasonable aesthetic choice (see the last half of this answer for real examples), but it's not a normal way of writing these words.
Second of all, do you have a good reason to "translate"? ナイトフォール・アカデミー is often a reasonable option especially when your manga is set up in a western city.
If you do have a reason to translate this and write it in katakana, ハクボ (薄暮) is a relatively uncommon word and your Japanese audience may not be able to catch the meaning instantly without kanji (and some may not be able to explain the meaning even with kanji). ヒグレ (日暮) and タソガレ (黄昏) are common words.