Why do some US universities have "Electrical Engineering" and "Computer Engineering" vs. "Electrical Engineering and Computer Science" departments?
It's usually politics or prestige.

Back in the days when the computer science discipline was heating up (mid to late 1990s), there was a big discussion on where to put computer science. Traditionally, it was a science, but at that time the economic outlook for high-tech (which included electrical engineering and computer engineering) was really, really hot, and it was fashionable to have a department that encompassed "everything high tech". Thus, there was a big push to move computer science to the Faculty of Engineering. This was augmented at the time by the birth of "software engineering" programs and by a number of papers discussing programming and software development as more "engineering design" than "science".

Fast-forward twenty years or so, and you have what we have now, where programs that are related to "high-tech" are roughly grouped together.

As stated already, the disciplines are different. I won't repeat @TinActon's words since he's summarized them well. However, they operated under the same high-tech umbrella for a while.

Really, you don't choose the department - you choose a program, but it's more likely that there's synergistic (industrial) collaboration in a department that has EE, CE, and CS together, as the industries that hire in EE, CE, and CS tend to overlap a lot. However, that's not to say that there isn't cross-disciplinary opportunities for CS and the other science fields either. Biology and chemistry and physics all have a very high dependence on equipment and techniques developed in the EE/CE/CS side, and similarly EE/CE/CS benefit from the work being done in the sciences side.