Ok. I did my final paper for my BS on Alviso - just saying.
I lived on the water in the Bay for ten years. The Bay is not "flat;" the water slopes as the tide moves in and out. I knew the tides and how much comes in the Gate, and what the differences are in the tides as a function of time. Alviso would be at minor risk to a "tsunami" during a rainstorm at high tide. There is little to no way it would be at risk from a tsunami at low tide below "mean lower low water" (the definition of "sea level" for purposes of charting). The tides in the South Bay can be two and a half hours later than at the Gate and about 6" different in height at that point. Needless to say, the peaks are less of a difference than at maximum flow when those differences exceed a foot. If a tsunami hits when the gravitational tide is outgoing, it would take almost three hours for it to disperse over the San Francisco Bay as far as Alviso. The reason is that the height of a tidal wave at sea is almost unnoticeable. The only reason it gathers in height is when the wave base strikes land, just like a regular beach wave. The pulse of water in a tidal wave is too short in duration to supply sufficient water to raise the Bay level by more than a foot by the time you get that far from the Gate. Therefore, chances are Alviso would be unharmed - just saying.
As to Alviso as a port, the reason it was uneconomic even for bulk goods was the cost of labor. One had to load and unload the boat and then load and unload another mode of transportation to get the goods to or from another location. Rail put those goods closer to town centers and they were dominant for that reason. By 1879 there was even a train to Los Gatos. Needless to say, the water coming into Alviso is also very shallow, making it a challenge for the few specialized barge-tug systems to navigate without running aground. When the tide went out, they had to wait. That put a limit on traffic. There were losses from loads running aground and costs of maintenance for barges that twist and bow under load if they have to sit on the bottom. The reason I know that is because I restored antique boats during that ten years of living on the Bay (including George Shima, the wheelhouse of which is now in the San Francisco Maritime Museum, which was a tug named after the owner that ran potato barges up to the Delta, also shallow water).
BTW, the reason I put "tsunami" in quotes is that our wondrous academics decided for us the unwashed that the term "tidal wave" was inaccurate in describing a seismic wave and therefore adopted the Japanese term for a seismically induced wave. Little did they know that the term "tsunami" translates directly to "tidal wave."