Depends on your strategy. Most say Siam, but I've always been partial to Greece. Siam is undoubtedly king when it comes reaping benefits from friendly city-states, just need aesthetics + protection, but Greece is king with allying them. No one can collect city-states like Pokemon like Greece can. With the right religious tenets and social policies, Greece can quickly monopolize city-states, leading to an early game advantage. I think it's patronage opener (25%), same religion (+25%), and Hellenic League (+50%). City-states are practically collect and forget for the Greeks and it can be very difficult to pry one loose from their influence if they finish patronage. Plus, I just like Greece anyway, their music and versatility. No idea why Greece is so dogged on these forums, they're one of my favorite civs.
So far, the only city-state civ I haven't played yet is Austria. I can't really knock on them much since I haven't tried them, but I just don't see how their UA is so special. First you have to ally the city-state. Then, pay more gold to buy them. You can put that gold towards your own settler which brings me to my final gripe about Austria: The map generator lurvs to put city-states in awkward city locations. Maybe it's my OCD, but it's a huge pet peeve to me when I see a city-state built one tile off the coast or a large river.
