Ignore the LA bashing.
I lived there for four years and moved away last June for a job, never thought I'd miss it this much. I grew up in CT/NY if that helps. LA is awesome. SF & SD are beautiful but LA is the place to be. Check out Venice beach for sure, Santa Monica, the usual Hollywood stuff, etc. Seriously if I were you I'd make the majority of my time in LA.
LOL, "majority of my time in LA"? Don't listen to this clown. Yeah, check out all that stuff, but unfortunately that'll take a day. Maybe two if you're really slow. Max.
Are you going to be spending anytime in San Diego? If so check out the following places:
Gas Lamp district. It is near the airport and convention center. There are lots of really good restuarants to go to and the place is alive almost any night.
Second this. Also check the waterfront. Really charming (a little fake and touristy, but it's better than the waste of time that is Fisherman's Wharf...)
Oh, and check out the SD zoo - it's fairly awesome. I abhor zoos, and even I admit the SD zoo is pretty cool - big open area for animals to roam around. You take a "safari" to see 'em.
And check out the old town, it's historic and not crowded at this time of the year, so you can take a look quick.
One more thing; once you get to San Diego, you can drop off your car and use the streetcars for a day - San Diego is astoundingly tiny, you can walk/use public transit to get to Gas Lamp, the zoo, the old town, and the airport. I'm assuming you're not public transportation-phobic, being from NYC and all.
Something else to think about, and this is just for the nostalgia.
Heading down to the Socal Basin on your way to San Diego, you'll be coming up on the end of Route 66. The bulk of it there is still as it was when it was in its heyday (IIRC, it ends at the intersection of the Alternate US 101), but you may have the time to drive part of it from there out to Pasadena or further out to the Inland Empire (Pomona, San Bernardino, etc.)
But at least you can see not only the classic cars, but part of the route that everyone used to take to get out west, before there was an Interstate.
BL.
Second this - and if you do this, make damn sure to stop at Foothill BBQ in Upland. Best. BBQ ribs. Ever. Hands ****ing down.
Didn't find SF all that great, to be honest. Maybe I spent too much time with hipsters trying to be ironic drinking PBR though in the Richmond district though.
That's like staying confined in the upper east side of Manhattan and saying Manhattan isn't all that great. Your loss, man.
Some of those places are within Los Angeles County not Los Angeles City. LOL.. I am heck you might as well include Lancaster and Palmdale for that matter! LOL.... But I agree there are some places that you probably don't want to go to....
Umm, but that's the thing - if you concentrate on the City of Los Angeles, you're left with basically nothing. As craptastic and sterile as LA is, it's only redeeming qualities lies in Los Angeles County, not the City itself.
Okay, enough bashing aside. Since you have 7 days to get from SF to SD, and that's about a 700 mile trip, here's what I'd recommend:
Day 1: Stay in SF the first day, visit Fisherman's Wharf and take a day trip (go with a tour company that picks you up, and shuttles you and returns you) into Napa Valley for wine testing.
I can't second this. Fisherman's Wharf is a tourist trap like no other. Walk past it to get an idea, then get the hell out.
I'll go contrary to the other guy above and say; use the majority of your stay in SF. It has the most to offer in all of the cities in California (disclaimer: not fact; opinion). Save your money by holding off renting the car when you arrive at SF - take BART into the city, and use public transportation to go anywhere you'd want to go within the city. You'll thank me - just like NYC, parking is hell + expensive, driving the streets is hell, and it's generally not worth it.
Things you should check out:
Powell/Union Square for shopping
Chinatown (make sure you walk up and down Grant AND Stockton. Grant is the touristy street while on Stockton you get the real thing).
The Embarcedero. Definitely go into the Ferry Building, it's awesome. If you are in town on a Saturday, go there in the morning and check out the farmers' market. Drink some Blue Bottle coffee, eat some lamb hotdogs, and have a good time.
If you don't mind kinda rough neighborhoods, check out the Tenderloin, on and around Laguna. Only go during the daytime though. There, try out some Vietnamese and Thai food. Definitely try a Banh Mi and Vietnamese iced coffee. FTW all around.
Check out Washington Square. Awesome Little Italy up there, still thriving unlike the (tragically) shriveled one in Manhattan. If you're up to eat at a restaurant and like garlic, eat at the Stinking Rose. Thank me later.
And make damn sure you check out the Castro. It's just a couple of blocks, but it's an awesome couple of blocks. Grab a coffee at the Castro Coffee Company and take a stroll up and down the street before hopping back on the subway to continue your tour
If you like Dim Sum; Yank Sing on Spear St (at the Embarcedero) is a must-go. But if you want to save some money, check out Dol Ho off Stockton. Not pretty to look at, but full of locals, good dim sum, and the prices are unbelievable.
If you like Guinness, that's the *only* reason you'd bother to go west into the Richmond. There's a bar there named Star and Pough, that serves the best Guinness I've ever tasted outside of Ireland. I'm not exaggerating. It's *that* ****ing good.
There's so much more; awesome restaurants, places to see (yes I'm a foodie

), too many to list here, but I think I got some of the better/easier to access places.
*EDIT* Oh yeah, and if you got the time, check out Rainbow Grocery. It's the hippest supermarket you'll ever see.
Once you're ready to see the Twin Peaks, Golden Gate Bridge, Muir Woods, etc (yes they are must-go's), grab the rented car and get at it. While all of those places are technically accessible with public transportation, it's more of a hassle (buses!) and if you're going to rent a car anyway, might as well use it. Plenty of parking at those places, too, especially during a non-touristy season like March.
Couldn't agree more. Stay out of Mexico right now if you can. Just go down to SD and have a good time. No need to go to Mexico.
This. Don't be a fool, stay safe. Mexico ain't Canada.