Thor's powers are not magic based. Kevin Feige confirmed that magic doesn't exist in the MCU and that it is all based on quantum physics.
http://screenrant.com/kevin-feige-doctor-strange-acide-trip-cosmos-degrasse-tyson/
http://www.aintitcool.com/node/49795
http://birthmoviesdeath.com/2014/03/13/kevin-feige-explains-how-magic-will-work-in-doctor-strange
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