Um, a multi megaton nuke of the city center would have the same effect or worse.
Also, I argue that your line-of-sight is increased by "low-altitude" EMP blasts (30 000 ft for a localized EMP on a bomber vs >100 000 ft for high-altitude EMP) whereas a nuclear detonation probably occurs at much lower altitude (~2 000 ft), so the higher altitude could in theory attack a much larger area as far as power is concerned. So in terms of electrical infrastructure, a larger area of damage could occur by Nike attacks on bombers higher up. But who knows.