Whatever scientists might develop, needs materials an external source of energy. Magic in most settings seems to pretty much pull the energy and mater from the hat. On the other hand, it is generally accepted that magic takes a lot of time to master, whereas science can just arm two battallions of grunts with cheap guns and point them towards the mage. So they are dependent on different resources, but I guess that in the long run, magic would win. Unless the war starts by the science faction taking out the magic learning institutions in a surprise attack.
If you go the Arcanum way, like DeadlyYellow suggested, then it's probably science. It seems that many mages in such a setting can be silenced by simply putting a big steam engine in the vicinity, so science faction's cities would be practically impossible to capture by the mages.
In some other settings where science and magic coexist, the former might actually run on the latter, an example being Wolsung. In those settings, science faction would probably win, since they tend to pack more of a punch, but risk losing the technology as a consequence of the conflict.
So yeah, I guess it all depends on what science/magic ideas you use. Especially with regards to magic, which can range from minor cantrips to nigh-divine power throughout settings.
