Which version of Dragon Quest 3 is the hardest?

Gameboy Colour or NES?

well considering the fact that the gameboy version eliminates having to open the menu so that you can search, open door, chest, and whatnot by just having you push the A button makes it alot more easier to play based on that fact that it would no longer be bery tedious, but as far as which is harder gameplay wise.. not sure

I'm going to say the NES version if only for the fact the game doesn't have the annoying glitch which makes your character go to max level after killing something like a slime in the mini-game.

I think the NES version, if only because of ancient gameplay mechanics. I think all the useless items that you find in pots were changed to stat-boosting seeds in the GBC version as well.