While I haven't ever worked with Expedia, I have heard a lot of reports that their customer service is less than acceptable. Apparently, they are not very responsive to your needs once they have your money, and have been reported to give their clients incorrect information. Again, this is all second-hand info, so take it with a grain of salt.
Also, make sure that you're comparing apples to apples. The quotes the
DCL website gives you usually include insurance and transfers by default, while Expedia's quote may be just for the cruise.
Finally, I'd suggest getting a quote from
Dreams Unlimited, the sponsors of this site. Their prices are very competitve, they are Disney experts, and their customer service is top-notch (this is first-hand info, based on my experience with them).
Good luck!