I am also riding a 29er these days. I haven't got to ride in the Boise area, so I can't help you with where to ride there. I have ridden in Stanely, Challis and the Salmon area. They all have lots of scenery and it is possible to get out and not run into anyone.
I used to ride in the Portland Oregon area and a friend has a website,
http://web.mac.com/kja78/Goride/Mt_Bikers.html , most of the riding is downhill/freeride but some scenic XC stuff too.