I would choose the 7D for a few reasons:

1. The effective maximum aperture of the 5D Mark II combo will be f/5.6 X 1.4 = 7.84, nearly f/8. This will somewhat cancel out the light-gathering advantage of the full frame camera.

2. You will still have a bit less effective reach with the full-frame camera, even considering the small pixel-count difference and even if you crop. Cropping always degrades image quality as well.

3. While the 400 f/5.6L is not a bad prime by any means, its image quality will noticeably suffer when using the 1.4X teleconverter (mouse over the image to see the differences), further reducing any seeming advantage of the full-frame setup. You would not much like the results with a 2X TC, let alone stacking TCs.

4. If 560mm is not enough reach, you will have "nowhere to go" with the full-frame setup, whereas on the 7D you can still slap on the teleconverter and likely get a much better result than you would by cropping the full-frame image. (And, remember, the 7D without the TC will have a bit longer effective reach than the 5D Mark II with the TC.)

5. Optical differences are hard to assess without comparing both in the field and filling the frame with the intended subject. Note however that besides the optical impact of the TC noted above, the 7D + naked 400 f/5.6L would be expected to have more consistent edge and corner performance than the 5D Mark II + 400 f/5.6L + 1.4X TC. Balancing this "sweet spot" effect of using a crop camera is that the lens will be challenged a bit more by the higher pixel density of the APS-C camera. Still, with such a high-quality prime, you will still get quite excellent results on the 7D wide open.

6. The 7D offers other advantages in autofocus, frame rate and build.

You may also note that the pixel-count difference here is nearly negligible, only about 300-400 pixels in each dimension. For all these reasons I'd lean toward the 7D, at least without a chance to field-test them both.