Could it have been an E-4B[1] or some new variant of it? That's the first thing I think of when reading large, white, unidentified plane. I remember seeing one on Sept 11 circling near Wright-Patt - very unsettling thing to see in person.
Living near Omaha, I see them all the time -- they look a lot like Air Force One (and get mistaken for that by non-locals all the time due to the similar livery). That's the first plane I thought of reading this article, too. I imagine that, while not being developed as true stealth aircraft, any variants developed of this plane would try hard to not show up on radar.
[1] https://en.m.wikipedia.org/wiki/Boeing_E-4