This is a very individual thing and depends on one's strength to weight ratio.
For me, pulldowns are the way to go.
Whenever I add pullups to my routine, it usually doesn't take long before I get an injury in my elbow. This is probably because of my 250lb bodyweight, which effectively means I'm always working in a heavy load range. Sooner or later a weak link gives out due to overtraining.
I don't have the benefit of starting out light and working up as I would in bench press, squats, deadlifts and of course pulldowns. If I had to start my bench workout at 250lbs, I wouldn't last long either.
If I do want to do pullups safely, I do it as the 2nd or 3rd exercise into my back workout when I'm very warmed up. (usually after rows and pulldowns). At that stage I'm only able to do sets of 5 - 8 reps and I'll stick to 3 or 4 sets.