don't really know alot about the area, but looking for a different type vacation for an eastern family. Are there any all inclusive resorts?
No, not that I am aware of.
How close to an airport?
The San Diego airport is right in the city. It borders the harbor and you can get anywhere quickly from there.
transportation provided or need to rent a car?
I would rent a car. There are some places a little north of San Diego (La Jolla, Carlsbad) that you will need to drive. Get ready for CA drivers and traffic!!
what are the beaches like?
It depends where you go. La Jolla and Carlsbad are very family friendly and clean. You can snorkel in The Cove in La Jolla, as well as see the seals. Mission bay is fun, but there's no waves, even though it is the ocean.
the ocean? (is it ugly like the eastern coast Atlantic)
It's not dirty or gross, IMO. I think it's cold and sometimes we have Red Tide (just a lot of kelp that makes it look red).
what is there to do with a 6 yr old? I know SD has a zoo, and there are various theme parks, but don't know how close they are to one another.
Sea World is awesome and right in Mission Bay (close to downtown SD). The Zoo is also great and very close to downtown San Diego. It is located in Balboa Park, which has tons of music, museums, entertainment, fountains, parks, etc. Free parking too!
Any and all info greatly appreciated !!