Best Separatist team for Padme?

It depends on what your plan is. Magnaguard will generally taunt until he dies and is more bulky, while Sun Fac only taunts when the ability triggers and has self-healing. Both of their counters can give Padme the undispellable Prot up, which can ruin the Spy attack, but that's better than Nute or Spy somehow dying to a second-wave onslaught.

I'd stick with Magnaguard for now. Both should work, though.