Dps-wise, Misa wins against some bosses, due to her decent pene (for a shooter), while Hermes dominates against high-def/immunity targets (since she relies solely on her extremely high raw attack + ignore def).
Not sure exactly what kind of content you would be aiming for, but for mid-end game I would say Hermes is probably a much safer bet at the moment. (edit: IF you are going for shooters, that is)
Apart from dpsing in raids, they also have other uses... like, Hermes is pretty decent for pvp (in fact she holds the 2nd highest win-rate in wxpvp), while Misa is pretty good for SCR (if you get lucky with the crits, you can kill one stone guy with two attack cycles, using just an average cannon and prin+steroid)
But really, just pick whichever you like the most