No. The 4.6L and 5.4L are not only different in size, but the engine management software is different. With a LOT of custom work you may be able to get it to run, but I suggest going aftermarket with a new system, such as Paxton, Procharger or anyone who makes a system for the 4.6L. The 5.4L is the more common engine to get aftermarket parts for, so you might be a bit hard pressed to find a good system for your 4.6L.
You can get better $ to HP ratios on getting other parts for the 4.6L such as upgraded heads, cam, and an assortment of parts. Depending on the miles on your 4.6L, you may want to spend $3-4K on a remaned 4.6L 3V engine. I see the odd one floating around on E-bay.
If you really want to supercharge, I do suggest going with the 5.4L as it is a stronger block and the pistons can handle moderate boost without any internal modifications. A stock 4.6L 2V may be able to handle at best 3-4psi without causing problems unless you upgraded the internals, then you can push the boost easily to 10+psi.
'00 Durango R/T 360ci 290hp (modded); 138,500m
'06 Pontiac G6 GT 3.5L 220hp; 44,000m
'12 Chrysler 200 Limited 3.6L 283hp; 13,000m
'99 Taurus 3.0L 2V Vulcan 145hp; 154,300m - Traded
Amsoil in all vehicles!