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.