Ruby Horsethief will be beautiful at the end of September and will definitely have enough water to float your boat. There might not be much current, but if you get on the water at a reasonable time (by early-mid afternoon), you'll be at Mee Canyon or Black Rocks enjoying happy hour within a few hours
. Count on another 2-3 hours from there to get to the Ranger station on your permit date and, if time permits, spend the night in the canyon before you run the rapids.
Have a blast!