I'm a fan of through-the-frame, simply because it allows you to build in less lift. You can always put longer shackles on to lift the truck or change the caster/pinion angle, but if you mount the shackles under the frame you're going to be limited in how much you can adjust the height of the truck.

Build in enough lift with the spring mounts to clear your steering gear, any additional height just puts the center of gravity of the truck higher than it needs to be. Move the axle forward and cut the fenders to fit whatever tire size you're aiming for.