Public transport is fine and easy.
You can definitely drive to the wharf or downtown easily as well - might be different driving than where you are from, but no biggie really. You can park at the garage at 5th and Mission for Yerba Buena, Union Square, even Ferry Building if you don't mind a little walk. Where near the presidio are you staying? If you can get to Geary, the 38 goes straight downtown. Garages are expensive I guess... I used to think that when I moved here 13 years ago, but now I'm like - oh great, under 30 bucks, that's a steal! If you are going to the big areas you can find a parking garage - other places, like say you want to go to the Mission or a smaller neighborhood, parking can be more challenging. You should easily be able to park in GGP too - but that is pretty close to the presidio so depending where you are staying you may more easily get a bus or walk.
Last year my kids were begging to do the hop on/off bus tour and we actually really enjoyed it! Their favorite is the golden gate fortune cookie factory in Ross Alley in Chinatown - they went there on a field trip and loved it! Just literally a small hole in the wall. Those cookies are yum.
I like the exploratorium better then the academy - looking forward to the new opening and will probably take our visitors there this summer.
Be sure to take a walk at Crissy Field when you are at the Disney museum. Best views in the city in my opinion when it's not foggy.
When are you coming? Please keep in mind in the summer it can be cold. And I mean like cold in the 50's. Especially on the west side of the city. Layers, layers, layers. No one ever wears shorts, unless it is super hot, and that is maybe like 1 day a year! Seriously it can be freezing especially near the water. Don't be an idiot tourist shivering in a tank top at the wharf. And the weather can change quickly - I never ever go anywhere without my fleece jacket - even when it seems warm and sunny - you go like 2 miles away, the fog rolls in, and BANG! Freezing.
Have fun!!
Kim