Can an illegal Immigrant travel within the US via plain?

I'm married to US citizen 6 years now. I just applied for green card couple weeks ago and still waiting for the answer (I'm not sure did they get my application yet). So now we would like to visit some friends in Boston. My passport from the country I'm born in is still valid but my visa in the passport expired 6 months ago. For us plain is the best traveling option but I'm afraid that they can see that my visa is not valid anymore and deport me because I am illegal.