I've been doing a lot of knockback spreadsheets lately, so I'm gonna unload a whole lot of that here right now. I use Final Destination as the basic guideline, just know that most stages are within 5% of its ceiling to bottom platform height, with Dreamland being around 20% higher, Dracula's Castle and Skyworld around 10% higher, and WarioWare and Yoshi's Story being about 10% lower.
You've got a lot of options for recovery, so be sure to mix them up effectively based on the situation at hand and patterns your opponent's displayed:
C4 Damage Boosting: Down-B, then Down B again to launch yourself. This is relatively quick (8 frames to drop it, 22 frames to detonate = 1/2 second) but WILL kill Snake on FD at 116% with no DI, around 130% with DI back, and around 120% with DI forward. This is probably gonna be your bread and butter for Cypher refreshes for low/mid percents, and it's also great for baiting out short range edgeguarding from the likes of Sheik. At high percents, though, it gets more and more likely that it'll just kill you anyway. There's also the problem of it dealing 17% fresh.
Grenade Damage Boosting: I feel like Rolex is the only Snake I see going for these, although he doesn't quite have the setup right nine times out of ten. The grenade explodes 98 frames (~1.8 seconds) after the input. At high percents, the grenade has great knockback for damage boosting, because it can't even KO Snake on FD until 196% with no DI. Use this to stall out a bit and get a second Cypher, but only when you DI into the corner, most other times, you'll just fall to your death. If you input the grenade while in the top blast zone and freefall, you'll be level with FD by the time it explodes, so use that as a gauge for when you can use this. You can get only a slight DI behind with this, so be wary of it. It deals out 12% fresh, so it's even more applicable for these situations.
Cypher: Is fantastic. Four frames of start up invincibility that shift to making Snake's whole body a hitbox, so it's awesome for going through quick aerials like Falco Dair or Sheik Fair. The cypher itself keeps a hitbox after you let go of it, making your getup a tad easier if you sweetspot with it (which you should if the chance arises) since its trajectory tends to catch ledge campers. It also rides ledges, so recovering from under FD makes your opponent work a lot harder to edgeguard you, especially if you can walltech their stagespike tries (which is relatively safe since shielding doesn't affect Cypher). As for sweetspotting: watch for the Cypher to just peek over the stage. That's the visual cue I use, and I rarely miss it. Fair out of Cypher is also really good, obviously: it's Snake's strongest horizontal knockback with hitboxes that cover Snake's entire height. It feels super safe.
Air Dodge: Know that you can't air dodge in your Cypher freefall, but you CAN after you cancel the Cypher with an attack. Your best options are C4 and Grenade, since they're way faster than any of Snake's aerials at 8 and 26 respectively. Check
http://smashboards.com/threads/snake-hitboxes-and-frame-data.339444/ to see how big of a deal that is vs. the aerials.
Grenades are also great for covering your return, either by throwing them early to clear space, or holding them late as you're getting back on stage to punish punishes. Percentages in general are HUGE for Snake's recovery options, though. Know what you can and can't do based on that. Outside that it's all fundamentals: save your second jump and know when you can just airdodge onto stage.