I've been through the same dilema. I looked at many of the 3rd party apple retailers who didn't charge tax and had free shipping. With the discount it came down to brass tacks. Especially going against that awful 8.5 percent tax... (political expletive). Without taking the time to crunch new numbers its usually not enough to risk dealing with a 3rd party. If I were you I would buy direct from apple with the discounted applecare. (don't forget to get your drives and RAM elswhere).
Having recently been in school I might recomend an alternative. Many students in creative fields (especially film, 3D, or VFX) feel they need the biggest and the baddest computer the first semester they are in school. Personally if I were starting out now I would start out smaller. I had to go back out to cali to finish one more semester of school this past year. My girlfriend who's still out there recently got the new aluminum iMac. This thing kicks ass. The processors are so freaking powerful now that you don't need to biggest and the baddest to start out.
I highly recommend this machine to students starting out. You can walk out the door with a full computer setup (and printer) for under 1500 that will get you through editing 101, photoshop for dummies, and aftereffects for poets. Then 2-3 years down the road when you really need some firepower for your thesis or whatever, you'll have that extra money, possibly invested wisely. I'm basing this on my experience in film school and assuming you're buying this for some kind of creative studies. So if you really want sound advice I would detail for the wise forum members what is you're studying and how far along you are. Especially for people headed to a freelance oriented field it makes so much freakin sense to have your biggest and baddest machine when you get out of school and really need it rather than when you're just starting out.
Its amazing how much you'll ramble on when you're waiting for the Fedex guy to get here with your new Mac Pro. Hope that helps a bit.
