Yes you can get an extended warranty from Microsoft even if you buy the S3 from Best Buy. I would highly suggest getting an extended warranty. It is only $99 and covers 2 accidental damages.
I would not suggest buying the Best Buy extended coverage because if you repair through Best Buy you will get non-Microsoft repair. Kind of like doing a squaretrade warranty. Your device will get repaired but it could be with different parts than what Microsoft uses.