Rob - the 100-400 will be useless indoors without relying on external flash (and focus assist beam). But f2.8 isn't much good if you need more DOF for boats - in which case flash is the answer. What exactly are you shooting indoors that you want 400mm for?
Outdoors,no question the 100-400 will outperform the 70-200 with 2x. It will be sharper and focus much faster. Plus it has IS which can be a bonus on a 400mm lens.