If I remember it good from another thread,the Holiday Inn at the Bay is with a direct view to the cruise ships and are offering packages, including parking.
Take a look at their website.
I´ve also heard about a Hampton Inn close to the pier.
Hope it helps
Marita, also in San Diego on may 6th, cruising on may 7th to Hawaii
I stayed at the Holiday Inn on the Bay. Woke up in the morning and looked out the window at the beautiful ship. We just wheeled our luggage across the street.