AKNick
640cc Uber Pimp
I've done both, and prefer the canopy glue because it cleans up better and has a harder hold than clear silicone. Because silicone has a rubberish feel when it's cured, when wiping down your plane with a towel will stick to it and rub it off potentially. You could fill larger gaps with silicone if needed, but the initial bond - RC56 for the win.