You definitely can't go wrong staying at The W.  Just be aware that Downtown San Diego is like every other downtown, one street will be good and the next one is dangerous.     
The Marriott on Shelter Island is also pet friendly and on the water.     
Mission Valley and Fashion Valley are good areas if you aren't sure what you want to do while you are in SD.  They are centrally located to most things with all 3 freeways being really close by.  The Zoo and Sea World are less than 10 minutes from there (be aware though that neither place has facilities for watching dogs while you visit).    
Dog Beach is fun, but tends to be an attraction for bigger dogs.  Mission Bay has lots of walking trails that leashed dogs are welcome on.     
				__________________    Don't get your knickers in a knot.  Nothing is solved and it just makes you walk funny.        |