As far as values go, they are pretty equal.
Be wary of a used 100-400. Try it first. Some of the early ones were lacking in sharpness. They weren't bad, but later ones are said to be better. I've had both early and later, and noticed the same thing. A second issue to watch out for is the locking ring that holds the lens at any focal length. Unless it operates smoothly and lets the lens telescope smoothly, skip it! Its not a matter of lubrication, it loses ball bearings and must be replaced at a unusually high cost.
Used 100-400L's without box sell for about $800, maybe a little more on ebay, and the seller has to pay ebay fees out of that. I might be able to squeeze $1100 out of my near mint lens that is in excellent condition and is sharp. It still has the box and other stuff.
I paid $1610 for it in 2010.