FOT doesn't count, neither does FO2, not really and FO2 only had two faint craters, the larger of which might not be a crater at all. That just leaves two areas on the Fallout World Map. The Glow and between southern LA to San Diego. We know that the Glow was hit by mutliple nukes but look at the artwork it's a totally different sort of affair to the LA crater.
Given that the coast line has changed, the islands have mostly dissapeared and the area is sitting on the San Andreas Fault isn't it likely that the extremely large crater is due to tectonic movement. The bombings set off earthquakes, some of the coast line fell into the sea, possibly there was even a new volcano for a short time. That crater certainly looks more volcanic to me.
Surely dropping all those bombs would cause such changes to the landscape?