We can predict meteors
The major flaw in this scenario is that if a meteor large enough to cause a disaster on this scale were to strike, not only could we predict its path and date of arrival, but we could deflect (link is for asteroids but the same concept applies) it after realizing it was a threat. If this meteor could not be deflected for whatever reason, ex. we spotted it too late, people would still have time to evacuate the city when we determined a tsunami would occur. Erase bodies from the menu for now.
It would take a while to find the goo, but "disappear" is a strong word
If a city-scale tsunami occurred, you would see lots of pollution, and lots of murky water. Furthermore, any "gray goo", if it could survive in the vacuum of space, then the impact, then the water pollution, reached the city, it would simply appear as more pollution or waste. It could take weeks to months before a significant part of the city drains, and muck is cleared, leaving time for your organism to dissolve the rubble slowly, without being noticed. However, months is not enough time to consume an entire city; instead of "disappearing of the face of the Earth" expect "sterilized and slightly smaller"
Media doesn't matter
You mention how a media deadzone would prevent people from knowing about this organism; this is not true for two reasons.
- Disasters, especially larger ones, receive excess media coverage
- Aid workers would find the goo anyways, probably after it started to dissolve either a worker or an aid vehicle, regardless of the presence of media.
Goo slipping out is unlikely
Assuming the goo is like an algae, or some other collection of small organisms, the idea of controlled thought moving all of the species back into the sea is very hard to support. This could be explained if the organism(s) ran out of food, but as mentioned above, they won't.
Alternatively, the goo could stay in place, carpeting everything at an exponential rate. That way, it could still cause excessive problems without having to move out intelligently.