It depends on the setting.
If it is in a Wuxia style setting where ninjutsu is a very real and practical use of Ki/Chi and forms of magic, then the ninja should be a rogue with this kind of magic for concealment, extra damage, etc.
But, if we are going for a more anachronistic standpoint, then the ninja really is less suited for traps/thievery and is strictly for espionage and assassination. I would take examples of the Monk class and mix in some of the sneak attack functionality of the rogue, adding in proficiently fighting with improvised/simple/small weapons.
Traditionally the ninja were typically used to counter samurai (typically commissioned by other samurai who couldn't publicly challenge the target) and to kill their target by any means necessary. Many ninja were even current Samurai or Samurai who had become Ronin and now served as dishonorable mercenaries.
So, the ability to disarm a fighter(samurai) or puncture thick armor. So maybe a bonus to disarm with a kusagami or some other disarm-friendly monk weapon (kamas?) and then armor piercing, stealth, sneak attack, high crits, high mobility.
Yeah, I would play that.