Tricky. A heck of a lot hinges on the details of the alien enslavement - are we disposable fodder for their sugar mines, are we domestic servants, or maybe just pets? Will we have the opportunity at some point in the future to get free, either through legal and societal shifts or through some kind of revolt, or is this eternal? Will we learn lots of valuable technologies from the aliens, or are they so far beyond us that it's useless trying to make the leap directly? It's a total gamble - could be good in the long run, could be terrible. The nuclear war scenario, on the other hand, pretty much guarantees that we'll survive as a species and then rebuild over time. There won't be anything actively suppressing us. So that's the long-term "safe" option.

A pandemic only hurts humans while nuclear war would also destroy plant and animal life.

Nuclear war would also destroy a lot of infrastructure that a pandemic would leave intact. It's easier to rebuild if all the buildings are still there.