This report was just published yesterday by someone who cruised in late December, early January, on TripAdvisor:

En route home from a fantastic 10 days in the Galapagos. A combination of a few days on each of Santa Cruz and San Cristobal, with a 5 day cruise visiting Santiago, Rabida, Bartolomé, and Genovesa. On the whole, no sign of El Niño. Weather mostly sunny, and plenty of wildlife both above and below the water. Saw no dead animals, but one of the guides thought that some (and only some) of the marine iguanas at Puerto Egas were thinner than usual. The water temperature was warm but we still saw plenty of fish, sharks, turtles and a ray while snorkelling, and there were penguins on Bartolomé. Who knows what the next few months will bring, but so far there seems to be little effect from El Niño.

As El Niño conditions taper off by about May, it seems that Galapagos is likely to avoid the worst of this biggest El Niño event since 1997-98.