The 4.6 is an awful little engine. Good reliability, just very lacking in power. My '97 F150 had a 4.6, because that was the only V8 available that year. When I got my '99 with the 5.4, the power difference was amazing. Mileage was pretty good until I added bigger tires and a bigger exhaust. Still, if I was concerned about gas mileage, I wouldn't have had my foot in it all the time. It was a 4x4 Off Road package with a tow package. It had the electronic shift 4x4, which was awesome. I loved that truck. We used it like a truck. It towed our 23ft camper, horse trailers, went hunting, went to Mexico. Lived in sand, mud, snow, and rocks its entire life. That truck was the best, most problem free vehicle we ever owned. Ever.
Kept the '99 until 2016, when we bought an F250. The F150 motors now are all strong. The 5.0 is the only normally aspirated V8, and is way stronger than the 5.4. The 5.0 currently makes 395 BHP and 400lb/ft of torque. The 3.5 EcoBoost makes 375 BHP, but 470lb/ft of torque, which is why it feels so strong when it tows. No matter what you buy, you'll be happier with the new engine.
It will be hard to go wrong with a Ford truck.