What are the implications of marrying a Brazilian citizen who is still waiting for his permanent residency here in the United States?

If he is applying for permanent residence, it will be a long process but as long as he has a valid basis to remain in the US currently, it should not cause any issues for you to get married and be together. Additionally, if you do get married, he can probably get a green card much faster through you if you petition for him.

You should consult with an attorney to review all the facts and discuss what options you have. There are several potential issues.

It is not illegal for you to marry, but it may entail quite a lengthy process for him to secure a green card. In my practice I consult many clients with similar questions. You should schedule an appointment with a trusted attorney versed in immigration law before marrying and explore his visa paths. His current status is unclear from your question and so would need to be explored further. If he does not receive his green card via his mother then he would have to exit, marry, then re-enter U.S. based on a marriage visa.