I'm from San Diego and we are staying at the port the night before the cruise at the Sheraton. Part of the reason for chosing them was because they participate in the "park and cruise" program. (We wanted someplace to park the car for the week.) They provide a shuttle to the terminal.
I've not stayed there before, but I drove by a couple of weeks ago and it seemed alright. I've heard mixed reviews as to the quality though. It is a block or two off of the main road that runs beside the harbor and about 5-6 blocks down from where the Magic will dock. I wanted to be close enough that I could walk down to see the Magic in the morning.
The area itself didn't seem all that bad, at least during the day. There was no one hanging around. The homes in the immediate area (across from the entrance) were definitely lower income. But it just didn't strike me as somewhere to worry about.
I believe they participate in the "fly and cruise" program also, where they provide transfers from the airport and to the port terminal.