I received a response regarding photography at Alameda NAS.
"Photography and filming are allowed on streets and sidewalks as they are public property. If you are in the parking lot of a building then that would be considered private property and that is not allowed. We get a lot of photography etc. on the property so the security guard was probably just taking extra precaution. I will be sure to remind our security that they should only stop people when they are located on private property."
For those of you considering shooting here, parking your car in a parking lot designated for a public park and staying on the sidewalks and streets will hopefully not lead to contact with a security guard.