the 'alum advantage' you mention is true for all CUNY schools. For example, if you graduate with a BS/BA from any cuny school, that school would definitely give you special treatment when assessing your application. For this reason alone, I think it's a good idea to apply to your alma mater.
Secondly, about the new york advantage - that depends on what you want to do in your future. if you see yourself moving out of ny, then maybe getting a degree at a more 'well known' school would be to your advantage. if you prefer staying in nyc, you cannot go wrong with baruch. excellent job placement, excelent value, excellent location/atmosphere, stellar extra-curric programs.
i hope that helps any. I just graduated from Hunter with Honors and will be applying to baruchs APT MBA program (CIS/Econ dual major) for fall 2010. im taking the gmat in feb. wish me luck!