Fair use? If you're asking whether we think you will prevail in a lawsuit based on a fair use defense, the meter probably leans more toward your side than towards the copyright owners. That's because -- analyzing the four four fair use factors -- your segments are relatively short (the shorter the better), your use of the material is clearly for the purposes of commentary, and your project doesn't seem likely to have an effect on the potential market for the copyrighted works. As always, this is only speculation and the costs of fair use litigation may overwhelm principles of free speech.
P.S. Dept. If you're planning on posting your documentary online, keep in mind that copyright owners can use DMCA notices to wreak havoc.