"The Nazareth metropolis area has a population of approximately 210,000 of which over 125,000 (59%) are Israeli Arabs, and 85,000 are Israeli Jews (41%), making it the only urban area with over 50,000 residents in Israel where the majority of the population is Arabic.[68]"
Jerusalem is Israel's biggest city, and it does have 209,000 Muslims according to Wikipedia, which counts as Israel's largest Muslim population by city.
Edit: Ignoring Jerusalem, which I would imagine donates mostly from the Eastern section, Nazareth seems to be the biggest with 66,300. It's at least the biggest Arab city, as in not cohabiting with the Jews.