Location, location, location. LOL. The Wishes cruises leave from resorts near the Magic Kingdom and cruise the areas around the monorail resorts, Wilderness Lodge, and Fort Wilderness. You then take up a position in the lake in front of the Magic Kingdom and watch the Wishes MK fireworks show from there.
The Illuminations cruises leave from the resorts near Epcot (Boardwalk, Yacht/Beach Club) and cruise the lagoons in the Boardwalk and MGM areas before proceeding into Epcot and tying up under the Bridge from Great Britain to France to watch the evening's performance of Illuminations in Epcot.