I've used three rack set-ups in the Tacoma's I've had.
Rack #1 was a quickie, 2x4 build that I ended up using for more than ten years. It was based on a rectangle of upright 2x4s that laid in the bed. Uprights on the corners braced by mortised/tendon 2x4 at 45 degrees. I secured it in the bed with 2" webbing straps/ratcheting cams across the rectangle from side to side. I eventually retrofitted it with drop down wheels on the front, so that when I pulled it out of the bed the wheels dropped down and I could just walk away holding the back side of the rectangle, even with boats still tied on top. Pros: cheap, strong, easy in and out, ability to remove with boats mounted. Cons: the rectangle and wheels on the floor of the bed interfered with use of the bed for truck stuff--firewood, mulch, gravel, etc.; also, if you center the boats on the rack, or a little rear of center, there's a heck of a lot of boat hanging over the rear bumper.
Rack #2 was the Thule x-tra sport. Pricey, even when buying used. Pros: very strong, mount and dismount quickly, truck bed uncluttered, accepts Thule accessories. Cons: cost, can be noisie at highway speed unless you plug up the slot on the bars, which reduces flexibility in mounting accessories; if you happen to catch a fence or tree limb with the rack, it will damage the rails on the truck bed; same as #1 with boat hanging over the bumper; Thule accessories cost too much.
Rack #3 is a Leer cap-mounted Thule bar. Pros: sleep in the cap; gear storage more secure; but these are cap pros. The rack is there and works fine. Cons: I have to remove the cap when I need the truck bed for truck stuff, and no way to carry a boat (ah ha, I put the x-sporters back on); same as #1 for overhanging the bumper, span between racks much shorter than other solutions.
If I had a double cab, I would just use roof racks on the cab. That way, the bed is unrestricted and you can center boats over the vehicle, not the bed. I would keep the racks mounted either on the bed or on the cab. The twist between cab and bed makes it undesireable to put one bar on the cab and one on the bed, although people do.