Because I can use my PC to mine Bitcoin using the Scrypt algorithm. I use NiceHash. They have an option to select which algorithm we want to use. So I was wondering, once I get my Antminer S3, is it possible to point it to NiceHash's Scrypt stratum and mine using the Scrypt algorithm?
No. Bitcoin does not use Scrypt, so you cannot use something that mines Scrypt to mine Bitcoin. Furthermore, the Antminer S3 is a Bitcoin miner, it can only mine SHA256d coins, such as Bitcoin. So it cannot even use the Scrypt algorithm or mine any coins that use Scrypt.