The water in all streams will be low in September, but the Truckee will be a good bet; if you are patient, you can tie into some very good fish on the Truckee. I actually prefer fishing the North Fork of the Yuba River near Sierra City because it has less fishing pressure and in general is a prettier stream. You can park at Harrington's Inn in Sierra City and access a fly fishing-only section of the river by walking downstream and across a narrow meadow. Most of the fishing is pocket water with a scattering of large pools. The fish are not large but 15" or larger fish are not at all unusual.
For a guide with excellent knowledge of the Tahoe area contact Frank Pisciotta at http://www.cyberfly.com/