I have both a monk and a ninja in front lines (along with fighter) and a ranger in mid line with my 2 spell casters. This way I get 3 guys with critical hit potential (monk,ninja,ranger) the fighter for beserking damage. All my guys can do ranged attacks as alternate weapon. The major difference bewtween monk and ninja are as follows from what I can see at 12th level.
Monk (dwarf) = Martial Arts Bonus
= Damage Reduction (right now its 18% and I think
it applies to physical damage only)
= Critical Hit
= Psionic Spells
= Effective when Blinded
Ninja (human) = Thrown Weapon Bonus
= Critical Hit and Thrown Critical Hit
= Rogue Abilities of Lock Pick/Traps/Pick Pocket
= Alchemist Spells
In terms of effectiveness in combat both do about the same for damage and attacks per turn with punches and kicks. They tend to critical about the same as well. In ranged combat ninja fairs a bit better than Monk. For Spells I tend to build up their fighting first but any magic school can be good regardless of type. The Ninja has rogue skills while Monk has damage resistance. Thats the main area to look at, if you have no one to handle locks, traps, pick pocketing then go for the Ninja. If you want a good fighter type Monk is a good choice since they can take a pounding especially when certain abilities approach 100 and unlock special ones.
Or you can do what I did go for both and enjoy all the pluses.
