to summarize:
if you qualify for an edu. discount, order from apple if edu. discount + tax price is lower than un-discounted price.
otherwise, order from a "reputable" company without nationwide presence. i ordered from j&r which is a NY company and i live in MI. it ended up $10 or so more expensive than apple's edu price but apple didn't have the machine in stock and j&r did, so i went with j&r.
if you want BTO, you generally have to order from apple.