I think the Gibson tone is more iconic but it doesn't matter to me what guitar he's playing, it's gonna be great whatever he plays.
I'd say his best tone for his style was the late 80's. The flanger gave him the added emotional girth he needed, and the dynamics of the Fender over the Gibson balanced perfectly.
My favorite is lace sensor strat into dual Soldano SLO's...
I like both. This has always been one of my favorite EC Strat moments.