Is the master chief an alien?

Yes, Master Chief, aka SPARTAN-117, aka John-117, is a human. Albeit, he is a bio-medically, genetically, and mechanically enhanced human.

If you want the complete story behind Master Chief's origins, as well as the other SPARTANs' origins, find a copy of Halo: Fall of Reach. This tells how the SPARTANs came to be.