You left off the Maritime Museum - which is often overlooked but an incredible value and very interesting - plus they have a pilot boat harbor tour as a part of the admission that would more than cover your harbor cruise needs. The submarine is especially interesting as are the tall ships. Plus the views are great. You could do a few hours there and then head down the street to the Midway culminating with dinner at The Headquarters.
You also left off a place I always take out of town guests - the Cabrillo National Monument. Spectacular views, the best tide pools in San Diego and a great trail walk. A small but very good museum on the journey of Cabrillo and some interesting films especially on whale migration. Plus the old light house and adjoining building with a working lighthouse lamp. ABSOLUTELY worthwhile.
Seaport Village is a bit touristy and you could miss it. On the other hand, the new Headquarters District (repurposed Police Headquarters) which is adjacent has some excellent shops and even better food. Puesto is wonderful and very different than many of the other "Mexican" restaurants in the area. Don't miss the old jail and line up wall (great photo op).
I would not miss Torrey Pines State Beach and Park, especially in the early morning for a hike in the Park. While you are there, the Torrey Pines Glider Port is only a few minutes away and fascinating to see the para sailers jump off the cliff and fly around. Adjacent is the Salk Institute and Louis Kahn's fabulous buildings and court yard.
Balboa Park could take two or three days if you want to see every museum and garden. You need at least a half day, maybe a whole one. The Prado restaurant is great, especially for lunch (sit outside on the covered patio).
Don't know if I should say this, but despite the controversy, I do like Sea World. I liked it better before all the amusement rides - but still find the grounds to be very interesting (actually took a tour of the flora/plants) and the ability to see/touch rays, sea stars and interact with marine life (Penguins!) - other than the shows.
The Midway could easily take a half day by itself- very well done and very interesting.
I also love Coronado and find the Del worth seeing. I live in North San Diego and we drive to the Del, pay the ridiculous parking fee and use their beach which is the best groomed beach in San Diego.
If you like to walk, the Sea Wall at Tamarack (Carlsbad) is a great walk. We start at the sound end, walk to the north end, up the hill and back south on the coast highway, then repeat. You could combine it with a drive a bit further north to the Oceanside Pier, walk to the end and have a meal at Ruby's Diner.
The Wild Animal Safari is best in the winter when it is cooler - but a visit to San Diego is not complete without a visit to the Zoo. Albert's restaurant (in the zoo) is a nice way to break up a visit and the food is way better than the snack stands.
If you want to see some California History, you can also take the train up to San Juan Capistrano - the Mission there is worthwhile (best of the lot) and you could have a meal at the Cedar Creek Inn (across the street) and take the train back - all in a day (or less). The Mission and surrounding restaurants are all walking distance to the train. Plus the train passes over some of the most beautiful land owned by the government that is part of Camp Pendleton and otherwise inaccessible. Sit on the left side and enjoy the water views.
I'd skip Tijuana. Border towns are not "Mexico" and the time to get back over the border is a waste of time if you only have a week.
You don't say where you are staying. San Diego is a BIG area comprised of a lot of small communities. Plan your time wisely or you will spend a lot of time stuck in traffic.