The seasons of Peru is divided into its dry season and it's wet season. For the area surrounding the Salkantay Trek, which gets up to 4600m, the weather can be very changeable. Be prepared for whatever the season you go!
The dry season: Late April - Early October
The busiest time will be from May - September, but during then you'll have the best chance for good weather (however expect very cold nights, down to -6 degrees Celsius). However, even in the dry season, you should be prepared for rain as the weather can get very changeable at such high altitude.
The wet season: Late October - April
Shoulder months such as October/November and April would be a good time to go, with not too much rain and less people.
Once you head into December, January and February, the rain becomes quite intense with a majority of days raining (and raining a lot). As a bonus, there is less people during the wet seasons. We saw other hikers when we went in December but it was minimal and never ever felt crowded.
If you are going during the wet season, I recommend garbage-bagging everything inside your pack, even if you have a rain cover. Indivdually garbage bag your sleeping bag and clothes.
You can read through the story of our Salkantay Trek and how it rained everyday and soaked our sleeping bags. Itĺl help give you an idea of what to expect. And while it was immensely tough, it did make for one of the experiences we remember most vividly and fondly.