Vito is a composite, and he does have elements of Bonanno--both wanted their sons to succeed them, both had two close capos, one who betrayed them, the other who stayed loyal. For that matter, Vito, like Profaci, was the largest importer of olive oil in the US. But I think he's most like Costello for the reasons cited.
I don't see a connection between Clemenza and Profaci. Clemenza was under Vito for decades, and apparently stayed under Michael until he died. Profaci, as a young man, was made the Don of his family by Salvatore Maranzano after the Castellemmarese War of 1930-31 and remained the Don until his death in 1964.