Though for me they're both formidable villains with their own aspects, I have to say that Scar was a much better villain.
He killed Mufasa for starters, without even having blood on his paws. He manipulated the entire pride to believe that Mufasa's death was an accident, and told Simba that his father's death was his own fault, leading to Simba to develop a heroic blue screen of death (BSOD =
http://tvtropes.org/pmwiki/pmwiki.php/Main/HeroicBSOD). And this seemed to last for years since the next time we see Simba he's an adult, so probably around four-five years of age (since that's when lions reach their maturity). Now imagine for five years blaming yourself for your own father's death? Imagine how much psychological damage Simba received from that? Not only that, but when Simba returned Scar tried to turn the rest of the pride against Simba (and it probably would've succeeded if Scar hadn't slipped up).
Zira was insane, simple as that. She wanted to avenge Scar no matter what the cost was, even being abusive of her own cubs (Nuka definitely comes to mind). Cunning though her plan was to manipulate Simba's pride by accepting Kovu, and then have Kovu murder Simba in a moment of weakness, it doesn't match up to Scar's achievement, and overall her impact on the characters was hardly much compared to Scar's.
Zira was a good villain, but not really one that had an impact. Scar was definitely the better villain overall.