What are the current requirements? If you have your 12V and want a negative rail up to about 50mA, then one of the popular (but old) charge pump IC's like the ICL7660 will do. There are plenty of specific IC's for inverting converters, but if you want ultra cheap then a 555 with a couple of stage sof inverting charge pump will do. It all depends on the current required, allowable output ripple, and switching frequency. Note higher switching frequency doesn't necessarily mean higher efficiency - just smaller inductors/caps and "easier" filtering.
Generally the options are: inverting switcher (inductor), charge pump, DC/DC module, push-pull converter driving a tapped transformer, all the way to a full mains transformer with dual outputs.
The MC34063A is indeed a bit poo, but I've found it to get the job done, albeit with pretty poor efficiency and output ripple - how did you build these? Breadboard is a nono for SMPS.
The AP3211 appears to be a buck converter, these can sometimes be configured as inverting switchers, but not all are capable. Schematic for your setup?
You mention size restrains too - so what are they? And how many "units" ?