Whatever you do, you need to make sure that you have good evidence before you go around and make this HUGE accusation. This type of thing is a really touchy subject and putting something like this out in the open could be very detrimental to your family. I would probably just ask my mother who the father of the baby is. Be very careful how you bring it up, though. Try not to act like it is a huge deal that she is pregnant, because if she feels she needs to act defensive, the chances are that she will lie about who it is that got her pregnant. If there is any evidence of actual substance I'm sure that your moms sister will wonder about it as well. People tend to be very knowing when it come to things with their kids, and your aunts skepticism will probably take care of the worrying part for you.
Bringing something like this up to your extended family is accusational, to say the least. Chances are that people will get offended, rumors will start, and feelings will be hurt. For the time being I don't really see a reason for you to make this public.
Good luck with your family situation.
-------
:)