We estimated mountain whitefish abundance at a couple sites in Boise River during 2009 as part of long-term monitoring. All sites were upstream of Glenwood bridge. We have no recent sampling data farther downstream, but whitefish inhabit the river at least as far downstream as Middleton. During our survey work, we saw very high abundances (2400-2800 whitefish over 6") at the two "town"sites. These sites were approximately 1000 m in length. These sites were in the reach you mention but a little farther downstream from Barber Dam downstream to downtown Boise. Mountain whitefish are highly abundant throughout the Boise. I wouldn't recommend one area over another as long as you stay above Glenwood and below Barber Dam.
We also have very high whitefish abundances in the Payette River downstream of Black Canyon Dam, near the town of Horseshoe Bend, in the SF Payette near Garden Valley, and in the SF Boise downstream of Anderson Ranch.
If you have additional questions, please contact fisheries personnel at the southwest regional office at 465-8465.