Out of Wahweap:
#1: The Rock Creeks are kind of the jack-of-all trades in terms of anchorage possibilities, proximity to Wahweap, Dangling Rope, Rainbow Bridge, and some really good canyons on the southern shore that are great for exploring but tough to put a houseboat in (think Cathedral).
#2: West Canyon is long and beautiful, has some great beaches, and also has a "versatile" location that is semi-close to lots of places.
#3: If you can make it way up the San Juan, Piute Bay has some gems and you'll be skiing with Poseidon, Neptune, and all other gods of water.
Honorable mention: Mountain Sheep Canyon. It's not quite as beautiful as Cathedral (but it's not far off). Mountain Sheep does have some great anchorages for houseboats (usually many for smaller boats).
I (clearly) don't know the north end well enough to comment and I'm hardly a fisherman, so I'll let anyone who knows better tell me that my spots are rotten for fishing...I wouldn't know any better.