Take him with you instead. I want to say that the show is a little under an hour, but my 2 year old girl sat through the whole thing without even squirming, so I don't recall exactly. I suppose I should technically say she was 25 months, since a month or two makes a difference at this age. She also made it through the Golden Mickeys and Disney Dreams and loved them all.
Save Flounders for time that you want really alone to do stuff like the Art of Entertaining or the Imagineering presentations.