Seeing as this pertains to all generation Gym Leaders and not only those in HeartGold and SoulSilver, I'll just move this on over to General Pokémon Gaming.
For me though, I don't necessarily find any of the Gym Leaders to be difficult. I notice they do get harder as you progress, of course, but none in particular that is all that difficult to say. If I had to choose one, then it would probably be Clair of Johto, as Dragons can be tough to deal with at times, considering they only have two main weaknesses that not everyone trains. :\