I have been on both and they both have their pros and cons. I'll describe each separately:
Illuminations: The cruise starts at the Yacht and Beach club, sails to Hollywood Studios and then back to Epcot. No stops along the way. The captain gives fun facts about the resorts and parks. The viewing area is pretty much directly under the bridge that connects the United Kingdom pavilion to France. All the other cruise boats pulled up next to us, we were all side by side in a line. We had a very close, direct view of the fireworks, but obviously we couldn't see all of the nations light up.
Wishes: The cruise starts behind the Contemporary. It sails around Bay Lake, then into the Seven Seas Lagoon. Again, the captain gives fun facts about those resorts and the Magic Kingdom. The viewing area was in the lake, obviously, but with a clear view of the castle and fireworks. The sound was "piped" into the boat. The other cruise boats were farther apart and each tried to stake out the "best" location. Since we were in the lake, the view of the fireworks was from a distance. And the captain kept having to reposition the boat since we kept drifting. At times, I had to look behind me to see the fireworks because of how we drifted.
My personal opinions: I preferred the up-close view of the Illuminations show. However, we were very close to all the other boats. I mean, literally up next to them. That *may* spoil the magic of a private boat. I preferred the cruise part of the Wishes cruise. For me, I was more interested in the Magic Kingdom area than the Epcot area, so the fun facts were more fun to me.
Overall they were both great, so if I had to choose one, it would probably come down to a coin toss.