If you include Skye, try Dead Link Removed which is a b+B/self catering place run by a couple of photographers. I haven't tried the self catering, but the b+b is excellent! Superb waterside location just north of Broadford with easy access to the various tripod holes around the island.
Try http://www.uniquescotland.com - I've had cottages from them on Mull and at Glenelg. The North Cottage on the Eilanreach Estate near Glenelg is a particular favourite of mine.