After taking the Illuminations Cruise twice, I never thought Wishes could top it, but in the end I voted for the Wishes Cruise.
The view from the boat for Illuminations is spectacular, but not so very different from the view at several places around the World Showcase. Seeing Wishes from the water was a totally different experience. The only downside was that we couldn't hear the audio very well at first. Over the course of the show, we slowly moved closer to the MK, so the sound was almost as good as being in the park. As I understand it, some boats (the Magical Gathering boats) are actually equipped with an audio feed, but unfortunately none were running the night we saw it.
Another plus (I thought) was NOT being in the hub for Wishes. For some reason, every time I see it, I've ended up between two speakers that seem a little out of sync, perhaps because I was closer to one than the other. The result is rather garbled audio, and one speaker slightly overlaps the other. No such problem from the boat.
In the end, both cruises are AMAZING and you can't go wrong!
Doug