I'm guessing this has something to do with "queer" having political/social connotations in the West. Or maybe it's a difference of translation? I'm watching a sub release that uses the former but i've seen the latter used in various articles and on different websites.
This is purely a matter of different translators translating a word in different ways.
The Japanese word in question is バケネズミ（化鼠） bakenezumi. This can be taken as "monster rat1" (化物の鼠) or as "transformed rat" (化けた鼠). It is quite reasonable to translate bakenezumi as "Monster Rat", but it is also easy to see how a translator wishing to be a bit more flashy might choose the term "Queerrat" (with "queer" in the classical sense of "weird, peculiar", not the modern sense of "homosexual").
This latter choice makes some sense insofar as bakenezumi is (I believe) an original coining for From the New World, and so it is not a bad idea to coin an original English word to correspond to it.
It seems unlikely to me that the translators who chose "Queerrat" did so as a form of social commentary.
1 Technically, Japanese nezumi can refer to mice, rats, and a number of related rodenty organisms. If you've watched the entire show, you will understand why "rat" is the correct choice here.