We did the Wishes Cruise last Thursday and it was pretty cool. We got to see the Electrical Water Parade as well while we waited for fireworks.
Another couple that joined us on the cruise had done the Illum. cruise and said the ash and smoke from the fireworks was pretty intense. You're much closer to fireworks at Epcot that MK. Also, the boats line up side by side at Illum. and you have no sense of 'privacy' if that is important to you. Wishes is more spread out. Drawback to Wishes - not all boats have corresponding music piped in. We didn't, but could hear it from a neaby boat.