Keep in mind, mage dps will look like its coming up short if you just leave your DPS meter running the whole dungeon. The have a long wind up time as they have to apply scorch, get an ignite going, and get their instant Pyroblasts before they start cranking out their numbers. Normally on trash, you don't get that far, especially with DPS like shamans who start with an instant, then a quick gauranteed crit, and then a bunch of 1.5 second casts. No wind up time at all. It usually evens out on bosses, I find.

There's also an issue of gear. If your mages gear is lagging behind the others, your obviously going to see a gap in their DPS.