I read this in the 1990s, I think as a paperback. Aliens have taken over Earth. The main character lives with the aliens and does not consider himself as human, but as an oddly shaped alien. Somehow, he winds up in contact with some of the humans who are in rebellion, including an awkward sex scene where I remember the female kept referring to his "joystick". He learns how the humans are kept as livestock, involving what is essentially a pithing operation to ensure that they don't have higher brain function. For some reason, I want to say that either he or the aliens liken the livestock humans to pigs. The only other detail I remember is it being established that ruins of the major cities such as New York are now underwater... he's with the rebel female at the time, but I'm not certain if they're still in the alien ship, or if they're in their own ship.
I know that this is not I, Weapon which has a similar concept of humans raised as livestock, but a wholly different plotline.