I believe Yakima and Thule make tubular cross bars with brackets to fit our vehicle rails. It's a better, more versatile option than the curved Toyota cross bars for $185. Look at REI.com for these or do a search for Yakima or Thule. The two brands are virtually the same.
Rocky Road makes a utilitarian frame rack that bolts into the vehicle rails. It holds fuel cans, shovels, hi-lift jacks and anything else you can strap on. 4runner Roof Rack:Â*5th Gen 4Runner Roof Rack
I opted for a Baja Rack Utility Rack for a few dollars more. It's the full length of the roof and is flat on top for loading long gear and lumber, pipes, etc. when I'm working on this old house. The Standard Basket rack is shorter, less expensive and also a good option. Baja Rack: Home
Gobi makes the Stealth rack for the 4Runner. There are other brands of roof racks but these would be my favorites.