Even if you buy at Best Buy, you can always buy AppleCare so long as you're still within the limited warranty period of the laptop. It isn't something that has to be purchased at the same time as the laptop.
I don't know if that helps tip the scales one way or the other, but it's something you should know. Also, be sure to read the fine print on those same as cash deals. Usually, if you don't pay the balance in full before the end of the grace period, they retroactively apply a pretty nasty interest rate on the full purchase price. You have to remember that it's a business, and they're looking to make money. They aren't offering outstanding terms out of the kindness of their hearts.
And the best buy store warranty is only good at best buy, but applecare is good at any Apple store or AASP in the world. Of course the AppleCare won't cover things like liquid damage or accidental damage. Not sure if the Best Buy one does or not, but something to look into.
Generally speaking, when it comes to computers, I prefer to stick to manufacturer's warranties. It just kind of depends on who is offering the store warranty. Best Buy probably isn't going to screw around too much, but a lot of times it can vary store by store what kind of service you're going to get. I work for a place similar to Best Buy's Geek Squad, and let's just say some of the stores you just know are going to be trouble. Just recently, I was going back and forth with some service manager for about a month. They kept insisting that a drive on a customer laptop needed to be replaced because it wouldn't read discs that they burned with it. After going back and forth 2-3 times, with a 3-4 day transit time each way, I finally proved to them that it was the el cheapo discs they were using as tests discs. I've had to embarrass a couple of other people. One person diagnosed a bad HDD, another a bad logic board, and I fixed it by reinstalling the OS. So, not all service techs are created equal, and even at Apple you'll take your chances. I've gone into some local Apple stores and gotten nothing but blank looks when I ask even a fairly simple technical question.
Put simply, retail is a brutal market. Most of the people with any actual skill will find a better job and leave as quickly as possible, so the people who hang around a long time are usually not the ones you want anywhere near your system. Management at the store level can change week to week with people being promoted, demoted, fired, moved to another store, etc.
So, I guess what I'm getting at here, is take a little time to get to know your local Best Buy and Apple Store store(s). Being a teacher, exploit your position a little and maybe ask some of the more technically inclined kids in your class (assuming they're old enough to be able to give you a worthwhile answer) what they think. Maybe ask other faculty members if they have any experience with either place. If your school has an IT person, they'd probably be a good one to ask. Forget things like customer service, focus in on things like how long it took for them to repair the system, what condition did it come back in, did they try and upsell you on a bunch of useless crap like AV software, was anything missing? If they got a look at the work area, what did it look like? Does it seem like there's a large number of systems to a rather small number of employees?
Take your time. A $1000 laptop is probably a big purchase for someone on a teacher's salary, so you want to make sure you have as much info as you can get before committing to one or the other.
I have a question, and I seem to keep going back and forth on it. I want to buy a MacBook. I am a teacher, so if I go to the Apple Store, I get about $100 off the price. Also, I can get Apple Care at the Apple Store. If I go to Best Buy, I don't get the $100 discount, but I get 18 months same-as-cash. At Best Buy there is no Apple Care, but I can buy the Geek Squad protection. Now I am wondering, is there something I am missing? Is there a benefit to one or the other that would tip the scales?