Well, the full report hasn't been released yet, which should explain the reasoning behind some of the findings.
As for eyewitness testimony,
this article is interesting. 13% of the witnesses interviewed for AA 587 said a wing fell off. Neither wing actually fell off, it was actually the vertical stabilizer.
And there are witnesses in the docket for the Colgan flight that say they saw the plane and there was no fire. Also, a lot of the comments about weird engine noises indicate it was right before the crash. There was around 30 seconds between losing control and the crash when the aircraft would have sounded odd due to the unusual attitudes and low altitude. What would be interesting would be strange engine sounds prior to the upset, which would have shown up on the CVR and DFDR.
As for a cover up, it doesn't really help Colgan all that much to say that it was their badly-performing pilot rather than, say, their badly-performing maintenance engineer. The NTSB hasn't shied against criticizing manufacturers before; why would Bombardier get a pass?