Yes, you get miles for those flights in the Alaska Airlines Mileage Plan but it is NOT elite qualifying miles, FYI. You can see this on the Alaska Airlines mileage plan page for Icelandair.

I wanted to book a flight on Icelandair actually SEA-ARN, the price was awesome and the connection was perfect but I'm going to book on DL/KLM instead because I want/need the Elite Qualifying Miles.

Bummer...maybe i'll get that stopover in KEF one of these days...