I think the Whistle Stop is it for the LA area if you are looking for a real train shops. You can always find the hobby shops that cater to the R/C and other hobbies and so happen to have some trains, but these tend to be the 'toy' trains.
Down south in the 'OC' we have Mile Post 38. They recently moved into a larger shop. Their narrow gauge inventory continues to grow. In addition to MP 38 there are a few others, once again with the 'toy' stuff.
The bottom line is being hurt by the internet. I know this is where i go for my major purchases.
Dennis