We did the cruise the last night of Fantasy in the Sky fireworks and have also done Illuminations. They are different in the sense that with Illuminations you're right there in the middle of everything so the music is loud, the fireworks are loud (very smoky too), but it's great as long as you don't mind that. My DD was 2 at the time and held her ears the whole time.
The MK cruise is more sedate. There's a little more sightseeing to do on this one. Both cruises take you for a 20-30 minute ride before stopping for the fireworks. With the MK cruise, you can't hear the music (well, you can a little). I remember our driver saying that with all the technology that WDW has, you think they'd pipe the music into the boats.
They are both a lot of fun. It just depends on if you're looking for a loud in-your-face kind of fun or a more laid-back kind of fun.