Between the Marriott by the convention center (on the waterfront) and the Marriott La Jolla, I would choose the downtown property. The view is wonderful and it is an easy walk to the Gaslamp Quarter with its wealth of restaurants as well as Seaport Village.
There are also Marriott properties on Coronado Island - and that is a beautiful place for a family vacation. I encourage you to go to the Marriott forum and check out reports on the various Marriott hotels in San Diego.