If endgame were still level 20, then a pair of EMGs would be a fair comparison. They are too weak beyond the mid levels of epics, unless one wants them for Improved deception with a powerful weapon in the main hand.
The named weapon that works well with ninja is the
Forester's Brush hook (formerly 19-20/3). In the past, that came out to 13-20/3 with the ninja expanded crit.
Here is my old screenie; this is no longer valid:
then with Divine Crusader:
(no longer valid)
The changes to Improved critical have altered this, making them 18-20x3 base; then, with the ninja enhancement, I guess this would be 15-20/3? Add IC: slash and they become 14-20/3? Then capstone for 14-20/4 plus vorpal?
Ninjas get great max dodge thanks to the changes to water stance, an ease in combining a dex-based range attack with melee (basically a drow star chucker/short sword wielder), a boost to melee power from Henshin, and incorporeality. I think that gives them better defenses than rogues, as well as faster speed (not by much) and abundant step.