D.M.
I agree with the previous posts that flights these days (no matter what day/time) are almost always full. We fly SFO to Boston once per year. (We also fly to Detroit once per year.) We have not had security lines in either direction that were longer than a 30 minute wait in like a decade. Usually they are more like 15 minutes. However, we do use the arrive 2 hours before the flight departure time rule, just in case. I've not experienced the "family line short-cut" others mentioned that often. Don't count on/expect that.
Flying out of San Jose is easier in may ways, since the airport is smaller and less crowded. However, when I have shopped for flights, I have found flying out of SFO usually costs less, and has a lot more more flight choices. That might just be because flights out of San Jose book up faster, since there are fewer flights to choose from. Maybe if you booked farther (months) in advance, the costs would be more similar. It is also easier to get direct flights if you fly out of SFO.
I disagree with the previous posts about advising you to take a red-eye. Our oldest was one of those kids that Benedryl hypes up. She wasn't hyperactive in general, but she was otherwise high-maintenance. We tried a red-eye when she was 3yo. She was too keyed up and only slept for an hour or two. However, since everyone else on the plane is trying to sleep, you get seriously annoyed looks (more so than usual) if your child cries or is otherwise loud. It's hard to even keep the overhead light on to read, for fear of keeping others awake. (Maybe I'm overly sensitive, but it really stresses me out to disturb the other passengers.)
I would recommend a direct flight if possible. They usually cost a bit more, but it is worth it in my opinion. You want to keep the overall travel time as short as possible. You also have to book the flight weeks in advance if you want to be sure to get seats together. Prices will also go up as you get closer to the travel date. Expedia.com is good for comparing prices and seeing the schedule choices, and it also lets you see how many seats are still available together before you book the flight. (And it does not cost more to book through them compared to on-line directly with the airline.)
Very few planes have the individual TVs in every seat back. Does your son have a DS? Do you have a laptop? You can buy a portable DVD player for under $200. I think you can also rent them. We take the approach of letting the kids have as much screen time as they want on the plane. I know that sounds bad, but it really helps keep the flight less stressful, for the child(ren) and parents. One movie, food and a nap will put you in pretty good shape. A second movie, or maybe an extra hour of something electronic and you will be golden. Having the option of more than one movie would be really helpful in case he doesn't take a nap. Trust me. We are generally pretty strict about limiting screen time. On a plane (or a long car drive) are reasonable exceptions.
Also, two of our kids have trouble with ear pain from the pressure change during the descent. That is when we break out the lollipops, gummy bears, or some other candy that you can dole out slowly, one every minute or two for the last 20 minutes of the flight. (The pilot will usually announce when you are about to start the descent; but if not, you can tell if you pay attention to when you first feel your own ears pop.) Swallowing often is what helps keep that problem in check. Again, if you are usually strict with sweets, this is a good time to make an exception. :)
Good luck!