I myself have had one hell of a time trying to pre-order FFXIV:ARR.
I first pre-ordered the game back in late-March, from Amazon.ca. They had sent me an e-mail telling me that FFXIV:ARR would be out April 30th...yeah, didn't happen. After the game wasn't released in April, they changed the release date to October 31st, but also switched the game's page to this:
"Currently unavailable"? And, even after the game was officially announced as being released August 27th, they didn't change the release date from October 31st. I actually e-mailed them a week after the date was announced, had to tell them when the release date was, and asked them if I was still going to receive the game. They replied two days later, basically saying "we'll look into it, and get back to you"...they never did. In fact, although they changed the release date on the game's page, my order still proclaimed I'd get it October 31st.
So, after getting no answers from them, I cancelled my pre-order with Amazon.ca, and checked with EB Games.ca. When I went to order the game, it said that it'd arrive in mid-September, at which point I didn't even bother ordering it.
Luckily, there's an EB Games just down the street from me, so I pre-ordered it face-to-face with them...but didn't get a pre-order code. I had to e-mail them, and they did finally send me a code, so good on them for that.
All that being said, two guys I know proclaim that Amazon.com has been efficient with his pre-order code and game information, so I'd say they're a good source. EB Games/GameSpot would be my choice, though you might have to rattle some chains to get a pre-order code...