It's a close race. Both were more of the made type fighter than elite talents. Both got to greatness thru hard work, desire, determination and toughness. Both formulated styles conducive to their physical abilities and skillsets. Lets not kid ourselves neither had some innate natural ability tho, otherwise they never would have made it. Elite level examples of what hard work can do for the right guys, if you have the fortitude.
If we're talking about natural ability and physical gifts, Holmes has the edge. He had natural timing, reflexes, and fluidity that provided a formidable platform upon which he could launch his armory. That said, mental composure, discipline, and maximizing potential, probably goes to Hopkins. He extracted every ounce from his body and mind over three decades.
Larry Holmes was made of tougher stuff then Hopkins and was overall physically gifted. similar to Ali but with a mean streak and some pop.
Hopkins was certainly much more versatile. As for naturally gifted, I'm not sure. Both were hard working, long reigning champions. It's not easy to rack up the amount of title defences that both did or fight well into their 40's.
If you're talking about gifts in terms of fluidity, relative speed etc then it's Holmes. Hopkins had a better mind for boxing imo but I'm not sure that counts as a natural 'gift'.