CNN rates the best Aviation Museums. Do you agree?

Hmm looks like they didn't go to many in the USA but they are not aviation oriented so they don't really know what to expect either. There are small ones that have very special exhibits and are locally supported not any corporate money or government sponsors either.
The one that houses the Spruce Goose in Oregon is one, the Boeing assembly line is not one its an industrial work place only. On Payne field outside of Everett WA where Boeing also builds airliners there is a museum that's not listed either. But the one in Seattle has more history than about any other in a wide scope of areas related to and part of aviation history since some took place right on the same field. IMHO only.

I've never thought that the Smithsonian's museum should ever be rated as #1. Do they have some interesting exhibits? Yes. But everything is so shut off from human interaction. This is why I love the USAF museum...quality AND quantity.

It's not a bad list. I would add the Technik Museum Speyer, although it's not purely aviation I'd also consider adding the Sinsheim Auto & Technik museum, which is the only place you will find both supersonic pax aircraft, a Concorde and a Tupolev TU-144, on display. The 747-400, donated by Lufthansa to the Speyer museum, is great fun since it's 30 m in the air and you can walk on the wings.