The stock manifolds on a Pontiac are quite restrictive, and headers do provide a significant performance improvement. The Ram Air manifolds (available reproduction) flow better than your standard manifolds, but still not as well as a good set of headers. I've run every type of header on my GTOs, from the old "Tri-Y" to good equal-length 4-tubes. I currently run Hooker SuperComps on my stuff, and they run extremely well (with the associated price tag).
Any header on a GTO with a Pontiac engine is no fun to install. Get a box of BandAids before doing the installation. Also, be aware that the headers will reduce your ground clearance, and they frequently leak. Be sure to bump your carb jetting up a couple of sizes to take advantage of the improved exhaust flow.