There are laws and there are the whims of a particular screener. My suggestions and opinions are mostly based on non-lawyer observations:
So, with regard to TSA:
-Can you videotape them?
-Can you just record audio?
-Can they legally ask/make you stop?
-If the above is "yes," can they then confiscate the recording?
You apparently can make any recording or take any pictures you want at a checkpoint except of the X-Ray screen image (TSA policy -- not law). If the confrontation is going down badly for them, you can bet that they will do everything necessary to tell you to stop or confiscate your camera phone. You can always bluff by telling them that confiscating the camera phone will do no good because the video is being sent to several remote servers. You can bet that they will up the ante pretty quickly and call over a cop.
With regard to LEO at a TSA checkpoint:
-Can you videotape them?
-Can you just record audio?
-Can they legally ask/make you stop?
-If the above is "yes," can they then confiscate the recording?
There are actually more safeguards concerning recording encounters with cops. Enough cops have been caught in the act (i.e.: The Rodney King cops) that most police cars have cameras that record every traffic stop. In the case of a checkpoint, I imagine that a cop would be more aggressive because he understands the stakes -- many of his brothers have gone down by being "caught" on tape.
I don't believe you have to tell them you are taping them. If I recall, a lot of the Rodney King footage came from a bystander whom wasn't noticed by the cops. If the cameraman had been doing anything improper, you would think that the judge would have thrown out the evidence of the videotape.
There was a pretty famous incident near St. Louis a few years ago. A 19 year-old kid was so tired of being pulled over and harassed by the local cops that he bought a camera for his own car. He taped a blatant incident of police harassment -- video and audio. The cop got fired and, I think, got some jail time. There were links to cop forum web pages, and most of the conversation revolved around how much the other cops wanted to torture and draw & quarter the guy.
So, I could be totally wrong, but my guess is that it's legal but the TSA and the cops would intimidate the daylights out of you. Fortunately, the kid in St. Louis had the guts to go through with it.