I am originally from Los Angeles, but live in Birmingham, AL with my husband, who has CF. I believe that the air quality does and will have an affect on lung function over time. Here the pollution is quite bad and we have air quality alert days when my husband can't go outside. There is a balance between having a good environment, but also having access to good medical care. If you have a job that pays well and you enjoy it, then it's worth dealing with the air quality.
Since you son is young I also recommend applying for insurance that will pay him when he's in the hospital. We have physicians mutual and you can have up to four policies. Depending upon the severity of your son's disease, he may not be able to work so having the income from the hospital stays will dramatically improve his quality of life. That being said, children born today have a great chance of making it past 40 and having totally normal lives.