I prefer a roof box over bags or a hitch basket. You can get a pretty low profile one that is made for skis that still has plenty of space as well as its nice on trips to put stuff that you don't need access to all the time (that stuff can be in the cargo area).
The hitch ones are nice, but I'm in and out of the cargo space too much for it to be practical. As well as since I go surf so much, the hatch is the best spot for rainy wetsuit changes.
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2001 4Runner 4WD Sport Package, Millennium silver, 110,000 miles, 2nd gen TRD Supercharger, Toytec BOSS coilovers, 890 OME rear springs, Bilstein 5125 rear shocks, custom Baldlands front bumper, PIAA 520 driving lights and fogs, 4x Innovation Sliders (welded on!), 18" Magnaflow muffler, JDM corners, 65" Thule bars, 20% tint, 16x8 FJ80 wheels on 265/75-16 Duratracs, Husky mats w/ cargo, rear diff breather mod, 3M clear bra, remote start, Pioneer AVIC-8200NEX