I would take niether one of these guys at their current points in career. If you are starting a frachise you need to get a good young QB to build around. Now if you are asking when they both were young guns, then Manning hands down for ability.
Starting a new franchise you have to take Manning (assuming of course you mean Peyton) because he is essentially a coach on the field. Brady is an awesome quarterback, but that is it. Manning would be great in any era. Brady is great in his current environent.