As captain, when you think about it, they were both made to look pretty ordinary without McGrath - Waugh at home against India in 2003/04, and Ponting in this current series. But I'd say Waugh was better. Loved his body language. Looking at him, you never knew whether he was winning or losing. I'm sure this had a calming influence on his men, both on the field and away on long tours.
As batsmen, I think technically Ponting is better. However, in the end, you have to go on who is the more dependable. I know it's a shockingly hackneyed cliche, but if there was one guy who you would get to bat for your life, it would be Steve Waugh. He was like Allan Border, in that he could chisel out runs, regardless of form, through sheer determination alone.