In the PC version of the game, are thieves better then Ninjas at disarming traps?

(I am assuming here that the PC version doesn't have any bugs with respect to this aspect of the game. Given how buggy certain ports of Wizardry games have turned out to be, I can't guarantee that there are none.)

The answer to the topic question is yes.

The answer to the question in your post is no, assuming equal level (which might not be a good assumption due to differences in leveling rates).

In Wizardry 1-5, the way it works is:
* To inspect a trap, the chance is 6 * Agility for thieves, 4 * agility for ninjas, capped at 95. This means that ninjas can't ever have more than an 72% chance of correctly identifying a chest trap. (The limit for ninjas is 88% in the SNES version, provided the ninja is a hobbit, because of the difference in how stat caps work (10 + racial minimun instead of a flat 18 across the board.)
* To disarm a trap, the chance is based off the character's level, with thieves and ninjas getting a +50 bonus.

(One tip: A character who has a stat maxed out has a significantly reduced chance (1/6 of normal) of the stat dropping at level up; for this reason, you might want your thief to *start* with 18 agility, even if 16 is enough to reach that 95% inspect chance.)

(Another thing: Keep in mind that the 2nd level Cleric spell CALFO gives you a 95% inspect chance regardless of the chest; hence, if you have enough casts of that spell level, a ninja might be good enough to deal with actually disarming the chest. In fact, it might be a good idea to get into the habit of using this spell, as some of the chest traps in Wizardry 5 are nasty, being able to permanently lower stats, destroy items, or turn a character straight to Ashes (do not pass Dead, do not collect a chance of being revived with DI).)

Thank you for that fantastic information dtgreene!

Just to make sure I understand you correctly, for *disarming* traps you say -->

"To disarm a trap, the chance is based off the character's level, with thieves and ninjas getting a +50 bonus. "

So if my thief or Ninja is level 16, then their chance to disarm is 16+50= 66%

is that correct?

It's not a strict percentage like that. I know that, for example, the dungeon level has an effect (though it's possible that, in Wizardry 5, different areas on the same floor may have different dungeon levels for this purpose; there's an area that's technically on the first floor, but has very powerful enemies (and can't be reached except through the deeper floors); that area might have a high dungeon level.).

What I can say is that a level 16 thief will have the same chance to disarm as a level 66 lord, for example.