I borrowed both 100-400 and 400/5.6L at the same time. I found the 400/5.6L to be a little sharper and well balanced and light enough that I could hand hold it on my 5D3 for awhile. Also worked great on a monopod. It's minimum focus distance is a pain and it is a bit longer. In short I honestly don't miss the IS with the 400/5.6L.
Never was that happy hand holding the 100-400's.
If you plan on shooting mostly on the 400mm end --- or longer with 1.4x tele-converter, I'd go 400/5.6L.
The 100-400L covers an awesome focal range. Great when shooting kids and insects that move close and far. The primes and shorter zooms may require attaching / detaching teleconverts to keep up.
If I had to chose one without any further information, I'd go 100-400.



