I was there at the end of September a few of years ago (took the next to last AA flt out of Cusco before they stopped). The weather was great. It didn't rain the six days I was there. Cusco and MP wasn't crowded at all.

If I remember correctly, it was cool in the morning, but warmed up in the afternoon. Make sure you bring the sun screen. You'll burn before you even feel it. You may want to take it easy the first day because of the high altitude. I had a headache that wouldn't go away the first day, no matter how much of that tea I drank.

The flight to Cusco from Lima was scenic. Going over the mountains, you saw the peaks above the cloud cover. I remember either Lima or Cusco had trouble with fog in the mornings, but I'm not sure which one. A lot of delayed flights.