Courtesy of the Library of Congress:
Looking southwest down market street in 1906 after the earthquake. The golden gate (sans bridge) is visible in the upper right. The destruction north of market is near total.
A view from Nob Hill, looking southwest. In the bay on the far left is Yerba Buena Island (I think). The fire burned almost everything down.
Let's move a few years ahead in time, to 1908. The following three photos were taken as the Great White Fleet, Teddy Roosevelt's burly new iteration of the U.S. Navy, cruised into San Francisco Bay. They stopped in San Francisco to refuel during their two year circumnavigation of the globe.
The ships of the fleet look like whitecaps on the distant bay. The photo seems to be taken from nearly the same position as the previous one: looking southwest, we see Yerba Buena island at the far left of the frame. Union square is the park with the statue on the lower right. This photo, taken two years after the fire, shows the extent of the city's recovery in that relatively short time.
The ships are more easily identified here, as they steam east along the northern coast of San Francisco through the golden gate. Aquatic park is on the left (I think). I can't quite make out Fort Point (aka Fort Winfield Scott) at the northern-most point of San Francisco.