Here we have an angle provided by CNN.
This shot is interesting for two reasons. First, it is from an angle very similar to the shot in question. Second, it captures a number of birds in flight. It is interesting to note how similar they look to the image in question and it is also interesting to note the altitude they are flying at.
Most importantly, of course, it is quite clear that there is no large dark object passing through or even near either tower.
