No knowledge of the hotel itself (Best Western Bayside Inn), but it looks to be in a decent area. The park-cruise-stay package sounds like a pretty decent one. Nearby Seaport Village is a fun place to shop and has a few restaurants as well.
I am a pilot for a major airline. We layover at the Holiday Inn On the Bay. That is close to where you will be. The area if very nice. If you aren't adverse to walking there are a great number of restaurants. If you are a beer drinker you can go to Broadway and walk up to Horten Plaza. Look for the Yard House (Broadway and 4th). It may have the best selection of beer on tap that I have ever seen. The food is also very good. Also there is the Gaslamp district for great restaurants and night life. Seaport Village, as was mentioned is also a good place to spend some time. All are in walking distance if you don't mind walking. I think the walk from Harbor Dr. to Horten Plaza is about 15 min. Also there is Anthony's Seafood Restaurant on Harbor Dr. across from the Holiday Inn. It has been around a long time and very nice.
If you like pizza, go to Filippis. The original is on India and not far from your hotel. It is a favorite in San Diego.