I go to every Niner/Seattle game since I moved to Seattle 10 years ago, I always pick visitor sideline as the end zone fans tend to be more aggressive, not Raiders agressive but more than I want to deal with.
Sideline, you can see everything that happens from a reasonable distance. If you are in the endzone, yeah it is cool to see it when they are at your endzone, but it is no fun squinting to see what is happening 100 yards away.