If you were talking about an apartment instead of a city, I would suggest roomy or spatial as antonyms for crowded. However, I don't think either one of those words works very well when describing a more sparsely populated city.
What I think you could use, though, (at least in some contexts) is the term breathing room:
Tokyo is a crowded city. Nagano has a lot more breathing room.
TFD lists “sufficient room for easy breathing or movement” as a definition of breathing room, with this example usage: “moved to the country to find breathing room.” A related expression is elbow room.
In a more formal context, a related term is population density (the population of a city divided by its area). Crowded cities have a high population density, while "uncrowded" cities have a relatively low population density.