My current party has three fighters. Two of which, I intend on changing into a Lord and Samurai. I was going to leave the third fighter alone. But now I am wondering if changing him into a Ninja is worth it? Will he fight better then the fighter after he regains some of his levels?

I know how to mix good and evil parties so this much is not an issue. Also, I know it is more common to turn a thief into a ninja but I would rather leave my thief alone.

Ninjas with equipment get three advantages over fighters (ignoring thief skills):
1. An extra attack (doesn't let you pass the cap of 10 attacks, so this is quite useful at typical levels, but disappears at higher levels due to slow leveling; I believe it may not stack with the minimum number of attacks certain endgame weapons give you) (Note that fighter-types get extra attacks every 5 levels; other classes get some extra attacks, but do so more slowly and only up to a limited number)
2. The ability to instant kill with an attack regardless of weapon type
3. The ability to equip katanas (but not the Master Katana, for whatever reason); note that Samurai can equip these as well

However, Ninjas have some disadvantages:
* Armor selection is more limited
* Ninjas level up more slowly; at higher levels, this results in the ninja falling behind eventually (exponential XP requirements mean this will only be a single level difference up to level 13, but once you get past that, the difference grows, and fighters reach 10 attacks much faster than ninjas, if you choose to level up that high)
* The most powerful weapon in Wizardry 5 can only be used by Lords (yes, even stronger than the strongest katana)
* A Ninja may be as good as an equal level Thief at disarming traps, but are significantly worse at inspecting them (in other words, they can't actually replace a Thief without the aid of CALFO)

Ninjas without equipment aren't that good. In particular:
* Unarmed attacks don't do that much damage compared to strong weapons (but you still get the instant kill chance); they don't even improve with level (at least not in Sir-Tech Wizardry; some of the Japanese spin-offs change this)
* AC improves slowly (starts at 8 and improves only every third level): to reach an unarmored AC of -10, your Ninja needs to be at least level 54, at which point it won't be too long before your Fighter reaches triple digit levels. Also, I believe you can't get this AC without a weapon equipped.
* Also, without armor, you don't get the magic resistance that the armor would give you.

Also, I should point out that you will typically not reach level 13 until rather late in the game, in my experience. (This isn't like some Japanese Wizardry spin-offs that take you to much higher levels, though there is an optional bonus area that can give you the XP needed at the cost of being quite dangerous.)

Ninjas have a chance of critical hits. They can also double as thieves. So definitely worth getting.
I think you can you can use an item (Dagger of Evil?) to turn a thief into a ninja without losing levels, unless that was only in Wiz 1.

Any class can critical hit with the right weapon equipped (though I haven't checked if mages have any options, and the earliest options for other classes are either Samurai only or cursed).
Ninjas can, at best, get a 72% chance of inspecting chests (88% on SNES for Hobbit thieves), and given how deadly traps are in Wizardry 5, those odds are not good. Hence, a party with a Ninja but no Thief will need someone to cast CALFO on every chest. (A thief with 16+ Agility has a 95% chance to inspect chests, as good as CALFO.)
Wizardry 5 has no class changing items; you only see that in Wizardry 1-3 and most (?) of the Japanese spinoffs. (On the other hand, Wizardry 5 *does* have IHALON for reducing age, so the age cost of class changing isn't an issue in the long run.)

Thank you for the information again dtgreene.

I hate winning a battle only to have the damn chest blow up in my face. No thank you. I will keep my thief. If I decide to put a ninja in my party, he will replace my fighter.

You're welcome.

By the way, one thing you can try is to have your thief inspect the chest and have someone cast CALFO on it; if they don't agree, cast CALFO again. The chance of both CALFO spells (or a CALFO and a 16+ Agility thief) failing is (assuming a good RNG) 1 in 400; the chance of them giving the same false ID is even smaller, so that should be pretty small.