I reproach to the thief to be only there for looting chests.
You have a choice:
- put your thief in the fourth slot where it does nothing 90% of the time and push a priest in the front slots,
- or put it in the frontslots where it has worse AC, worse weapons, worse hit points and worse to hit stat than the priest.

The thief should be a more martial character, that is:
- better weapons,
- or more swings,
- or ranged weapons,
- or double damage against the monsters who have less initiative than it.

The ninja is theoritaicaly an underwhelming martial character: worse weapons than samurai, worse armor than lord,
no spells, worse utility than thief for identifying traps (less than 75%).
It is a warrior with the hit points of of a thief and critical hit and better saving throws, but not the killing machine taunted by the manual.
For unarmed -4 AC, the ninja must be Lv 36; for unarmed strike 2d4 (5 +- 3) compared to 1d5 +10 (13 +- 2) with shuriken and 1d3 +9 (11 +- 1) with vorpal blade.

I suggest:
- (10 - (2*Lv/3)) AC in place of (8 - Lv/3) AC
- a flat bonus to critical hit while unarmed,10% to maximum of 60% (instead of ~0 to 50% maximum),
- a bonus to initiative ramping with Lv up to -3,
- or a bonus to unarmed damage growing with level to a maximum of 2d8 (9 +- 7),
- or like I suggested for the thief (double damage against the monsters who have less initiative than it.

Those suggestions, IMO, would change the game too much, and would be better served for a separate game rather than one that's supposed to be faithful to the original.

In Wizardry 1, everything a fighter can use is also usable by a ninja. Also, ninjas get an extra attack, which helps at low levels with poor equipment (which, unfortunately, is usually the time when you can't make a ninja because of the high start requirements).

For a thief, my recommendation is to raise the character to level 9 as a mage or priest first, then change to thief. You may have difficulty with trap inspection (unless you're playing the new remake, where class change doesn't lower stats), but CALFO can cover that role until 16 agility, and having access to spells will make the character not dead weight. Also, the early floors of the dungeon don't have interesting treasure.

This is to add to the thief's/ninja's abilities:

I've noticed that when fighting priests, bishops, and other monsters that cast divine spells, my thief tends to get silenced A LOT. Not that it matters that much for him because he doesn't cast spells at all, but how about receiving a bonus to the hide/ambush ability? If a character is silenced, it would be logical that hiding and ambushing would be much easier.