You can boil sterilize agar, but a PC is more certain.
I would not try to use a microwave to sterilize agar.
Boil over with agar causes a horrible mess and is very common. That is why you never fill a jar of agar to be pressure sterilized over 2/3 full.
A full jar of agar will boil over in the PC and cause an un-Godly mess.
More important than sterilizing the agar is how you pour and seal the Petri dishes. I strongly recommend Parafilm.
Here is a thread I did on making agar plates:
http://forums.mycotopia.net/agar-str...zai-style.html (Agar for the masses - Banzai Style!)