I have owned both, an '06 3500 with the 5.9 and now I have a '15 3500 with the 6.7. Hands down the 6.7 pulls waaaay better than the 5.9 and it's cleaner too. Of course I own a 2105 6.7 that uses DEF, really hard to compare the two. I will say the 5.9 puffed a bit of smoke leaving soot on the wheel fender where as the 6.7 using DEF leaves NO soot what so ever! The mileage is really close, although the '06 might have been a little easier on fuel than the new one but that's fine with me the difference in power more than makes up for the small difference in fuel mileage.
I think I'd get the '07 - '09 6.7 if for no other reason you'd get a 6 speed tranny instead of a 4 speed. IMHO the 6 speed is better than the 4 speed.
Dan