Get the 5.4, more power and torque, probably no worse on the fuel economy.
4.6 has no torque, never has. I can't believe they put something that weak in a full size truck. I drove a brand new '05 F150 4.6 for a little while (I put 1500 miles on it) as a rental and was thoroughly disappointed with the power. I ran a 0-60 on the G-tech, took 10.3 seconds. Pathetic! After a week I made the rental place give me something else, I couldn't handle it anymore. But I guess it's o.k. if you are used to slow trucks that get crappy gas mileage.
They replaced my rental F150 w/ a new Silverado 4.8 V8. The chevy 4.8 ran a 8.8 second 0-60 on my G-tech. Night and Day difference in torque and passing power. Even hauling a load in the back, night and day. And the chevy got better mileage to boot.
Not slamming Ford here, just that motor in that truck. For the record I drive a Ford.