I've played countless good Ikes, offline and online, so I know this MU fairly well.
In terms of close quarter combat, Ike does surprisingly well. Ike has an easy time pressuring Snake up-close with jabs, and can follow-up with various mix-ups depending on how the Snake is DIing. I.E: if the Snake is trying to DI up and jump out, you can SH (or full hop, depending on where he is) a bair. If he's DIing away, you can follow-up with a grab or Dash Attack. Ike has nice walling abilities - FFing fairs into jabs, properly spaced nairs, and spaced dash attacks are all comfortable approaches.
Ike's best approach on a nade happy Snake is spacing fairs and SH air-dodges. Learning how to z-throw (immediately throwing a nade back, in the air, with L/R/Z and your c-stick) is helpful too, but the Snake should be cooking his nades anyways. Apply pressure with fast falling all aerials, and grabs - Ike's bthrow is especially good at following up against Snake.
Ike has an okay time fighting Snake off-stage, but Snake gets away with a lot of stuff too. If you catch Snake recovering low/mid high, you have a few guaranteed fairs, so bait air-dodges and punish accordingly. If Snake recovers high, wait for an air-dodge and FF uair, or wait on the ground and charge a usmash (Snake WILL get hit by a perfectly timed usmash, and a nade will NOT save him... good luck predicting where he'll fall though :<).
In the end, fight Snake in the middle of the stage, and be weary of his ground control. In all honesty though, Ike does fairly well against Snake in a weird way, so this MU is no way impossible for him. I would have to say it's about 40:60 in Snake's favor.
