First of all, Dr. Zakir Naik is a** strict Salafi/Wahabi** (the movement that claims to follow the Pious predecessors, in reality they do not!), Majority agree that Dr. Zakir Naik is NOT a scholar. No doubt he’s an expert in comparitive religion but he should NOT be looked upon as a scholar who can answer your questions regarding Aqidah and other fields!! So just take the good and leave the doubtful (for that go to trusted scholars)
What he (Zakir) said about mazar and grave worshipping is correct, one should not go to a mazar and worship! He should just avoid these places because they lead to SHIRK!
Regarding building atop of graves is a matter that scholars have dealt with and have difference of opinion and we leave it to them. But our job is to not attend the mazaars and places where acts of shirk take place regularly..
Dr. Zakir Naik’s position on tawassul(wasila) is typical of Salafis in that they say nobody can intercede for us..!! Ofcourse the chosen ones (pious ones) can intercede for us if Allah wants them to!
Check out this link for definition and articles explaining** tawassul**: Isn’t Tawassul Just A Form Of Shirk?
Also please read the following for understanding if the Prophets are **alive **or not.