Reading thw writes up for it on Wikipedia, it seems as both are very accurate (as the write up for Unite 93 tells of many many things the same as in Flight 93) but the two main differences are, I belive, that Unite 93 is set in real time : as in the entire movie is exactly the same length of time as the take off to crash landing of the actual flight. This means tho that the films ends just before the plane crash lands (as it is all based in as much fact as possible, there's no real telling what happened at the point of impact), and also it deals with the passengers as a group, rather than focussing on individuals, as per the families wishes when consent was given to the film.

Flight 93 finshes AFTER the crash landing, tho you never see it actually crash, you see the indication it crashed, and the reactions of firefighters and the families to the crash. The film bases it self heavily on certain passengers and official people, and uses real dialogue from the film, and in some cases, what sounds like actual recordings of voices.

I've not seen United 93 yet, and probably won't do now untill October as I think it's out of the cinema now.....