Your decision on where to stay depends on many factors like what are you planning to do, your budget, and your arrival time.
If you are planning to mainly explore downtown, then you should consider one of the hotels right in the Gaslamp Quarter or downtown waterfront. Some of the best choices are the Marriott Marquis Marina, Hilton Bayfront, and Grand Hyatt. For a budget hotel in or close to downtown, you can try Porto Vista, Wyndham Bayside, or Westin.
If your main goal is to visit SeaWorld, then try the Hilton San Diego Resort & Spa, Hyatt Regency Masson Bay or the Bahia Resort. For budget choices, try places like Holiday Inn Express, Wyndham Garden, or Travel Lodge SeaWorld.