I've been out to San Diego for work conferences three times. The first trip I mountain biked, and I hit Mission Trails twice, Sweetwater twice, and Sycamore Canyon once. I may or may not have ridden from a high school parking lot through a military zone to get to Sycamore Canyon
I hear Noble Canyon is the shit, but I didn't make it out there. Of the places I went, I liked Sweetwater the best, but I would suggest you go to Noble Canyon based on what I've heard. On that trip I shipped my bike out there.
I rented a road bike from The Bike Revolution on the second trip and was very satisfied, but I don't know if they rent mountain bikes.
My third time in San Diego, having done both mountain biking and road biking on the two previous trips, I drove up to Orange County to do some riding. I rented a bike from The Path bike shop which I highly recommend, and I rode Whiting Ranch, Trabuco Canyon/Holy Jim, and the San Juan Trail. Whiting Ranch was good and right in town, but the other two were amazing.
I'm going to be out there for a weekend in March, but I'll be with the wife so I probably won't be riding.