My top two choices are Pat's and Loa Malnati thin crust - as a specialty treat I like O'Fame's Tomato, Olive Oil and Garlic on their crust -
750 W Webster Ave, Chicago, IL
Lou Malnati's Pizzeria
6649 N Lincoln Ave, Lincolnwood, IL 60712
2679 N Lincoln Ave, Chicago, IL 60614
Last I ordered there were some serious delivery issues that weren't rectified to my satisfaction, but...when it's on(and I suppose if you eat it there) O'Fame's delicious. My favorite is the thin crust cheese with garlic, tomatoes, and basil. Simple, perfect. Lou Malnati's ranks with Due and Gino's East(did I just write that?) as my favorite deep dish...the aforementioned in descending order. I do not care for their thin. It's way too soppy, sweet-ish, cornmealy Midwestern for my taste.
I really love Candlelite in Rogers Park on Western/Howard. Cracker thin crust and good sauce. Unfortunately, they do not deliver. I think Tuesday nights are buy one get one free.
I also second Lou's thin crust. They also offer LF cheese that I SWEAR tastes full fat.
O'fame is also very tasty.