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Their ways of sneaking around are quite different. Where Snake infiltrates secretly and unnoticed, Altair blends in with the crowds of the cities.
Snake fought on even terms with Cyborg Ninja Gray Fox in hand to hand combat as well as hold his own against Gray Fox when he used his sword. In H2H combat, I think Altair could put up a good fight, but he ultimately won't last against Snake's super-soldier prowess (He could dodge bulets in his prime, so throwing knives won't be much harder).
Whoever this "Al" is, I'll take your word for it. But Altair wouldn't survive ten minutes against Solid Snake with or without his weapons.
This isn't unlike Solid Snake vs. Sam Fisher, which is just an "Everything you can do, I can do better" case. In this case, Solid Snake has no problems doing everything that Altair does that would matter in a fight, only he's just better at it. Snake can dance right through Altair's swordplay (as I just said, Snake took on Gray Fox in MGS1, fighting to a draw when Gray Fox used his sword, and eventually overcoming him in hand-to-hand, and Altair has nothing on Gray Fox), can do any of the disarms that Altair can do, and has outstanding reflexes.