No expert in this matter - But expecting our first in the next couple of days.
I remember my wife being given some medication that softens the uterus, when flying anything over 6hrs. Give your wifes gyno a shout - I'm sure they will point you in the right direction.
I am flight crew for a major Asian airline & we are happy to take women after 13-14 weeks. However, as previously mentioned, I would reccommend having a browse through then CC forums.
All the best, good luck & congratulations
HPC