In terms of pure voice, I'd say Rafi > Kishore > Sonu. I think Rafi had the purest voice of any desi singer I ever heard. The thing is though, I always thought Kishore was more versatile than Rafi and Sonu. I think Rafi and Sonu have that classic "soft" voice that sounds like honey in your ears. Kishore perhaps didn't have as good a voice as them, but he could adapt better to sing various types of songs. He could sing a soft romantic ballad like "Yeh Shaam Mastani" or "Pal Pal Dil Ke Pas", but could also be equally effective singing fun, fast-beat songs like "Khaike Pan Banaras Wala" or "Apni toh jaisay taisay".
Don't get me wrong, I'm not saying Rafi and Sonu weren't/aren't versatile. I'm just saying that Kishore's overall body of work is more versatile than theirs IMO.