I never had to stay at any hotel since we lived there, but there are dog friendly outdoor malls in Carlsbad and Otay Ranch (down in Chula Vista near the border).
I found this online that lists the hotels and attractions where dogs are welcome.
DogFriendly.com's City Guide: San Diego, California
Which part of SD are you planning on staying in (north or south)? I can steer you towards some nicer areas from that list.