Neither, IMO. State doesn't make sense: do you go by origination or destination? Year is better, but maybe not ideal. Ultimately, it's your collection, so organize in a way that appeals to you. But my recommendation would be to organize by the obvious, and that's by CAM (or AM or ATS) number.
The fun thing about collecting is that you can collect and arrange by whatever method you personally enjoy. That said, most Contract Air Mail route first flight collectors use the well organized and established system that lists every CAM cover in the American Air Mail Catalogs. This is done by CAM route number. Using this system can make your collecting more easily understood by other first flight cover collectors and by dealers, and it can be easier to understand for yourself as to which legs of which routes you have and which you will want to look for in your collecting.