My first choice would be through Apple, but with all the problems with going through Apple this year, I had resorted to going through AT&T. All in all I'd feel comfortable pre-ordering through either...
Last year I ordered online from Apple, and received a phone on schedule. This year I pre-ordered through Best Buy, and will receive a phone someday. Not tomorrow, of course, but it'll get here. Sometime. In the future. You'll see.
That being said I might do something crazy next year, and order directly from Apple again.