He is better then just real good. Abilities: Nick Fury has trained as a paratrooper, Ranger, demolitions expert and vehicle specialist. He holds an unlimited-tonnage, all-seas license as a commander of ocean-going vessels. Fury has completed Green and Black Beret Special Forces training, and has been an agent of the OSS (Office of Special Services) and a liaison of the M5 (British Secret Intelligence). He is a seasoned unarmed- and armed-combat expert, was a heavyweight boxer in the Army, and holds a black belt in Tae Kwan Do and a brown belt in Jiu Jitsu. Fury has honed his fighting skills sparring with Captain America, perhaps the world's finest unarmed-combat expert. Fury ingests the Infinity Formula annually, slowing the process of aging in his body
In terms of pure skill Snake-eyes is a monster. His skill with a blade is so good that he was able to stab between parallel muscles of the heart with out cause any damange... he did this on a dime while he was running. Heck the guy even stopped the "Blade of Inexoriable" motion (mostly a chi amping feet but still good)! Snake-eyes is the finest living combantant (prehaps the finiest ever) of the Arashikage ninja clan... and that is saying something. Short of characters like Stick, there isn't a single Marvel character that could match Snake-eyes in skill.
Well, as most of us already know, Snake Eyes is the type that can sneak up on someone in broad daylight, on a gravel road, in the middle of nowhere. Fury's pretty hardcore, and has been know to hang with Cap during sparring, but can he hang with someone like Snake Eyes? I personally doubt it. He could give him a fight, but he wouldn't last.