American AAdvantage is the clear choice for one world- and in my opinion the best FF program.
For star alliance, CO or UA. She should pick the one that she will be flying the most.
Sky team would be DL, but in all honesty I would try to concentrate on one of the above One World and Star Alliance programs for the bulk of my flying and try to get a high status level in that program.
Sky team does not offer the global coverage that *alliance and One World do.
If I were living in New York and a frequent business traveler, I `d make it a priority to get AA Ex Plat status.