Phone is the best. And I also prefer not to use a TA - not because there aren't some good ones out there, but Disney makes it so easy that I just don't see the need for a go-between; I like that I can call Disney and make a change in an instant, and not have to wait for someone else to do it, relay information, etc., etc.
The reason phone is better than online is two-fold :
1) Disney's booking engine is notoriously bad. It won't help you get the best deal, it goes down a lot, and there are complications with payment that are very limiting because...
2) Money paid online is non-transferable and you can't add to it later.
What this means is, let's say you decide you need to change the dates of your vacation to a week earlier than you already booked. If you call Disney, no problem, they will simply take your previous deposit, apply it to the new ressie, and you are all set (providing there is availability, of course).
If you book online, however, you can't just call up and make a change. They have to refund your original deposit, and you have to pay a new one in the meantime (so essentially you pay a double deposit). I ran into an issue with this because they "lost" my refunded deposit once; it took three phone calls and several e-mails to get my original deposit refunded properly.
Doing it on the phone gives you more options, and there is less worry, IMHO. This is coming from someone who does virtually EVERYTHING online - bank, pay bills, etc. It's just easier to deal with Disney via phone, and the "on hold" music ain't bad.
NED