Right now I am using polyester, but am considering changing to cotton. From what I have been told, the polyester is a stronger thread and eventually will wear down the cotton fabric over time. The cotton is a compatible thread and will actually help the quilt last longer.
It might depend on whether you want your quilt to last until the baby grows up or for 100 years! If it is going to be well used and loved, it probably does not matter.
I also would like to hear what everyone else thinks on this topic.