For me, D'Onofrio's Kingpin comes off as frightening because he's damaged and thus slightly unpredictable. At times I found him almost whiny and childlike which worked really well for the development and backstory.

But MCD was purposefully violent because he enjoyed it and over all a much more simple take on the character. Plus he had the physicality to back it up and I found him over all more charming which is why he's the version I prefer.