According to information I can find, the Inca Trail is fully booked until October. For this reason it's always wise to book ahead if you fully intend to take the most popular trails. Although not the height of the season, September is still busy, and the weather is perfect. On the other hand, you will probably pay lass when you book on site. The risk is that the hike you are planning is sold out, nevertheless there are always other hikes available. The Lares and Salcantay trails are not limited by the Inca Trail Permits, so chances are you will get space on one of these locally, but no guarantees of course.
Keep in mind that only some Inca Trail treks bring you into Machu Picchu by way of the Puerta del Sol (Lares and Salcantay do not). This is the highlight for most trekkers, so make sure you read the itinerary carefully to make sure you are getting what you expect.
http://www.incatrailperu.com/ is a non-commercial site with tons of relevant information.