How is this compared to the N64 versions? What are the pros and cons? All I know is N64 version had gotten better ratings, but don't have any clue why.

Better ratings?! It probably got reviewed more, but the PC version was always the better version of the two. The higher resolution, graphics and sound alone give it a clear advantage.

N64 version ran at a resolution of 320x240, or 640x480 if you had the Expansion Pak. Reviews mention it had occasional framerate issues in both modes (worse in 640x480). EDIT: after watching a few 640x480 gameplay videos it looks like it was sub-30fps the majority of the time, with further drops caused by smoke and explosions.

PC version supports up to 1280x1024 resolution (or even higher if you use nGlide), with an unlocked framerate (60fps or higher is easily achievable on modern hardware). You can force antialiasing and texture filtering through your graphics drivers if desired. PC supports keyboard and mouse, joysticks and gamepads for input (note: some people seem to be having issues rebinding joystick controls).

I'm not sure if there are any differences in models, textures, sound quality, etc. (it's hard to tell looking at 480p YouTube videos of the N64 version...).
Draw distance is the same in both versions.

Here's a screenshot of the PC version running through nGlide (1440x1080, 16xS antialiasing, running at 120fps): http://i4.minus.com/ifnUiDz6xMR7o.jpg. One of the nice benefits of nGlide over the default Direct3D renderer is 32-bit colour (and better handling of transparent textures).
Unfortunately nGlide makes the game crash after each mission (at least on my retail CD version of the game) - progress still gets saved, though.

The cheat codes are also different between the versions. The PC version doesn't support the Buick, although it contains the data for it (I remember many years ago someone was able to mod it into the game).

You can read up over here on how to get it working.