"Czekam na brata" is the correct form. In the Polish language verb and preposition collocations are strictly defined ("Czekać na ...", "Należeć do...", "Dbać o..."), moreover the collocation is always connected with an exact grammatical case. So:
"Czekam na (kogo?/co? = accusative) -> brata"
"Czekam na (kogo?/co? = accusative) -> siostrę
"Czekam na (kogo?/co? = accusative) -> snieg
Of course accusatives demand different endings (brata, siotrę, śnieg), depending on the word.
You have a similar situation with "Gdzie są toalety". The expression "Gdzie są" is always connected with the nominative case. Some examples:
Gdzie są (kto?/co? = nominative) -> toalety?
Gdzie są (kto?/co? = nominative) -> dziewczyny?
Gdzie są (kto?co? = nominative) -> książki?
So, just tu sumarize; polish verb and preposition collocations are always connected with a given case. A good way to deal with it, is to memorize the whole expression. Btw, I know how this painful is, because I am trying to manage with German Die Rektion des Verbs, which works similarly.