Gamestop has announced that they are no longer able to offer Launch Day consoles and Amazon is now show all of their offerings (even bundles) as unavailable. Best Buy appears to have them available on their site, available for in-store pickup on launch day, but who knows how long that’s going to last. Right now I would say that the best place to get your pre-order is the same place I got mine, Sony themselves. One thing to remember is that being forced to buy a 3 month membership to Plus is not a bad idea, $15 will get you a free game on launch day.
On a related front, it would appear there are plenty of Day One XBOX One’s available at Gamestop still.