Reach can be good, but flexibility is best. The 200-400 is great for reach but if the whale breaches 30ft from the boat, all you get is a piece of the body. Happened to me more than a few times. That's why I like the 80-400 range. The great thing about the D2x is that you can go to HSC mode and gain 0.5x extension in a crunch. It's more difficult to use the AF points and it's 6.7mp vs the full resolution but you get the shot. And if you have the 70-200VR or 100-300f4, it's at f2.8 and f4.
The best way to shoot whale shots from a small boat is to shoot with high shutterspeed. Better yet for the D2X to get the mirror up so mirror slap isn't a factor, although I doubt it works with continous drive shooting. If you are having trouble with getting sharp shots with the D2X, try turning off predictive AF (function A4). The function assumes your subject will move and guesses which way, which can muck up the shot if you are shooting wide open.
For example,all shot handheld:

Shot at 400mm, f9 1/800. Not the sharpest, even with VR. Bad choice of shutterspeed and shot mode.

Here at 400mm, f8 1/1500. Much sharper. VR is off. Pumping up the ISO helps, but with the D2X anything more than ISO 800 will result in loss of detail with NR on or noise with NR off.
Peter
I didn't say there was a problem with a lens with a TC. I'm saying that stopping down gives better results in terms of sharpness. The 70-200 is sharp at 2.8 but sharper at 5.6. With a TC, it's now a f4, so stopping down to f8 would get the better result.