Illness affected performance - but not that much? In my second semester of sophomore year, I was moderately sick for most of the semester. It was not life-threatening, but I often could not attend class because I didn't feel well. As a result, I was behind and had to work a lot to keep up. My research output was significantly lowered during this period also, for the same reasons.

However, it's not like my semester was bad - my GPA was lower than usual, but from a 4.0 to a 3.9. My research was lessened, but I still did some productive work. It's just that it turned a perhaps stellar semester (at least, a semester in line with the rest) to a perhaps good one. One slightly less great semester might not matter much for some grad schools, but I'm aiming for top ones as well. Is this something I could ask my advisors to note in their letters?
I'd leave it out. This certainly doesn't sound like a bad semester that needs to be explained away. Being able to do well under adverse health conditions isn't really something you want to use as a selling point. Stick to what you did, not what you think you could have done.

If you mention it, there's a risk that someone on the admission committee will wonder if your illness is going to come back, maybe worse this time, and affect your work in grad school. They should not consider that, but people are human, so they might.

Congratulations, and glad you're feeling better.