This has been driving me crazy, but I want to say the Aztecs because they were more advanced, had a developed system of writing, etc. Any thoughts?
Civilizations aren't in a race with a single goal at the end. You can't just take two and ask what is more advanced. Each had a background and developed their own advancements through their history. Being an empire isn't a final destination for civilizations either. The classic Maya and the ancient Greeks are common examples of civilizations that weren't unified in a single state, but were instead small city-states and the territory they controlled united only by language, religion and a common history.
As for what was closer to an empire... an empire is, by definition, a large tract of land inhabited by multiple ethnicities that is ruled by a single government. The Inca Empire was exactly that, with the Inca himself being that sole government. The Aztec Empire was in theory a confederation of three cities - Tenochtitlan, Tlacopan and Texcoco - that formed the Triple Alliance, although Tenochtitlan and its ruler was the most powerful one. If only for that, the Inca was closer to the definition of 'empire', but that has no relation to being more or less "advanced" than anyone else, be it politically, economically, technologically or militarily.
That would depend on whether you mean an economic empire or a territorial empire, wouldn't it?