You can use 아니라고 or 아니라는 것은 (or 것을). For example, 1. A는 B가 아니라고 알고 있어요. 2. A는 B가 아니라는 건[or 걸] 알아요 [알고 있어요]. (1) sounds plain without a particular nuance while (2) is more confident (like adding "for a fact"). So here are different ways to translate "I know very well that animals are not objects.". 1. 동물들은 물건이 아니라고 잘 알아요. (strange) 2. 동물들이 물건이 아니라는 건[걸] 잘 알아요 [알고 있어요]. (sounds like mentioning a plain fact casually) 3. 동물들은 물건이 아니라는 건[걸] 잘 알아요 [알고 있어요]. (more focused on the subject 동물들) -라고 잘 알아요 is unnatural because 잘 means you're quite familiar with it but -라고 알아요/알고 있어요 sounds like you just happen to know this - the two parts don't work together well. Also, you generally use 이/가 for the subject of a noun clause such as "...-(이)라는 것". If you need to emphasize or contrast the subject with somethings else, you can use 은/는 as in (3). That is, (2) is more about the fact itself while (3) puts more focus on the subject 동물들.

"동물들이 물건이 아니라는 점은 잘 알고 있어요." This means "I know that animals aren't things well." If "동물들이" was "동물들은," then the subject of "잘 알고 있어요" is also thought to be animals, not "I," so it's better to use "동물들이." This is somehow subtle usage of 은/는, that bends the subject more tightly and closely to verbs of the sentenc. 민수가 산에 올라가서 걱정됐다. →I was afraid of Minsu that he had gone on the mountain. 민수는 산에 올라가서 걱정됐다. →this sounds more like: Minsu started to get afraid as he had gone on the mountain.