Having not played a significant number of great shooters on the NEC powerhouse, I'm not nearly qualified to answer as best I could, however, I'll answer based on what I own.
Also, top 5 is not nearly enough
R-Type >The game that got me to buy the system, legendary shooter which I swooned over in the arcade.
Blazing Lazers > Still one of my favorite shooters of all time. It just that good to me.
Lords of Thunder > Truthfully a tie between LoT and GoT as they are both epic, However LoT gets a bump for the totally bad ass and unique premise/design.
Gate of Thunder > Just awesome, could probably have used a smidge more variety in levels but holy hell, what a masterfully crafted game.
Spriggan > My love for Compile burns bright and Spriggan is Blazing Lazers (god why couldn't they just call it Gunhed) turned up to "11." So happy I finally have this in my library.
My continued list.
Download > Really, really awesome game which I just got recently and am enjoying quite a lot. Hard as nails but oh so cool.
Spriggan Mk. 2 > Very different from Spriggan but wow what a game. For a shooter the production values are fantastic.
Nexzr> I think this game, if I can ever pass the 2nd stage will go higher on my list, but as it stands its kicking my ass. And I'm enjoying it
Sapphire> A masterpiece and glimpse of what the PC Engine/AC could do. It is a shame more could not be accomplished on this config. of hardware.