Oh boy is it more expensive. You need to custom build just about everything for the 5.4... It will have more power, but neither would be a direct swap to corvette killer. Not only that, but you need to assess what you want from the build. Best bet if you're looking for something to replace your engine with: 03/04 cobra longblock. That will get you the closest and also give you plenty of space to grow. Other 4v's will still be limited by the bottom end, so no matter what you do, unless you go for the cobra, you'll have to strengthen the internals as well.
If you really want something to knock people's socks off, get the MMR 351R block, use GT supercar heads and twin turbo it (plus the 20k in supporting mods). At 1500+ rwhp you'll be ripping past Corvettes like they're standing still.
There is no cheap way to make a car fast. (I know you didn't ask what was cheapest)
how much $$$ you want to spend? 5.4's aren't all that great and dont have much more potential that the 4.6. the vette has so many advantages, so you have to figure out how you want to go about leveling the playing field. the easiest, cheapest, and probably the best way to go about it is adding a power adder of your choice.
I'd go with an aluminator 4.6 to drop some weight up front and a tubular k with a whipple 2.3. Honestly, the way to beat a vette is to have a better balanced car than a vette. If you make a horsepower crazy car that is not nimble and can take turns, the vette has just taken you over its knee and whipped you. Everyone is concerned with straight line power, and only those that really want a great car are concerned with making it balanced.
I dont think a 5.4 dohc is a lot more expensive than a 4.6 its just harder to get parts for, but an NA mod motor is expensive either way. If you are wanting more power a better question would be "My budget is $$$$, what power adder should I go with?" I think if you are going to add a supercharger/turbo you are better off staying with the 4.6. What vette are you trying to beat and what kind of money can you spend on making your car faster?