Physical Greninja I believe is BETTER than the Special Greninja
First of all, I haven't seen anyone else post this move spread or build yet for Greninja, so let me put this out for people to look at.
Item: Life Orb
Nature: Naive (+Speed / -SpDefense)
EVs: 252 Attack / 12 SpA / 244 Speed
IVs: If you can get 6IVs... do it. Otherwise sacrifice Special Defense IV.
Move 1: Ice Beam
Move 2: Low Kick
Move 3: Gunk Shot
Move 4: Water Shuriken
To understand why this build IMO is better, you have to do your research on match-ups. We all know Greninja is a "Glass Cannon". Greninja needs to hit first and needs a 1KO if at all possible.
So... lets look at the moves.
Ice Beam over Ice Punch!!! This is NOT obvious to most people, especially when building a Physical Greninja. However, when you begin to compare the moves side by side with the Pokemon the move is intended to 1KO... Ice Beam actually performs better than Ice Punch, even with only 12 EVs of investment in Special Attack. For most Flying or Dragon types, either move will be dangerous. But when you look at Landorus-T for example, Ice Beam achieves the 1KO where Ice Punch doesn't. Look at Mega Pinsir. Same thing. Besides those two Pokemon, the remaining weak to Ice Pokemon are 1KO by either move. So overall, Ice Beam is better and still does the job it is supposed to do. Additionally, any opponent that sees Greninja use Ice Beam is going to assume it is the Special version and likely carrying the common moves that the Special version is known to carry (e.g. Dark Pulse, Scald, etc.)
Low Kick! What a incredible coverage move this provides for Greninja. You can now hit Pokemon that most people don't expect Greninja to handle. It hits Ferrothorn hard. It can 1KO Mega Gyarados, Heatran, Hydreigon, Mega-Lucario, Magnezone, Mamoswine, Mega-Sharpedo, Terrakion, Mega-Tyranitar, and can potentially 1KO Mega-Kangaskhan. There are others of course that this hits hard, but I'll skip the list. Look it up!
Gunk Shot. This provides great coverage and hits Fairy types super-effectively. You can 1KO Mega-Abomasnow, Mega-Alakazam, Mega-Altaria, Mega-Gardevoir, Volcarona, Sylveon and several others. It also becomes your strongest damaging move against other Pokemon like Politoad, Raikou, Rotom-W, and actually hits Goodra harder than Ice Beam or Ice Punch.
Finally... Water Shuriken. This move is often overlooked in favor of the more common and well known Water moves that Greninja has access too (Scald, Hydro Pump, Surf, Waterfall). After you add up all the coverage you already have from the first 3 moves and what you can already 1KO or hit hard with those first 3 moves... you now have to consider what forth move provides the most value for that forth slot. Greninja suffers from 4-move slot syndrome. So many other nice moves to pick from. I've reviewed the other moves Greninja has access too, and compared them to what additional value they may add. In my opinion, Water Shuriken provides the most value over the other options. Why? Greninja suffers from being a glass cannon. Opposing Pokemon that have priority moves or can out-speed Greninja are going to reduce Greninja to being inconsequential. Take a Gale Wings Talonflame for example. Greninja could carry a move that would 1KO Talonflame, but the Brave Bird that Greninja is going to take to the face is going to kill Greninja before you can do anything. So, the need for a Priority move suddenly becomes incredibly useful. Talonflame can be 1KO with a 4 or 5 instance Water Shuriken. With tied priority with Brave Bird... if their Talonflame isn't Choice Scarfed... suddenly your priority move goes first because Greninja's speed is simply higher. Take Blaziken for example. Blaziken's "Speed Boost" ability is going to cause Blaziken to out-speed Greninja. But with Water Shuriken and priority... suddenly you can get some damage in that super effects Blaziken before it hits you back... and you have the potential to 1KO Blaziken with this move.
There are other Pokemon that out speed Greninja including Crobat, Noivern, and Aerodactyl for example. Although Greninja can carry a move that can 1KO these Pokemon, it is mostly pointless if that other Pokemon out-speeds you. Water Shuriken can potentially 1KO Mega-Aerodactyl. So would you rather get some damage in or would you rather just die? I'd rather get some damage in if I'm going to run Greninja on any team.
Mostly, it is best to use Greninja as a late-game sweeper. If you can bring Greninja in against Pokemon that are already injured, and you can finish them off with a priority move, this provides utility, especially if that injured Pokemon normally runs priority moves of its own. Sure Low Kick can 1KO Kangaskhan, but if you're hit by Sucker Punch first, then it wouldn't matter. If you can finish off a 1/3rd health Kangaskhan with a priority move of your own, you win!
This is all just one person's opinion obviously. If you'd rather try to hit a Gengar with Shadow Sneak... then by all means use that as your priority move. Or if you feel you really need some other move... then go ahead and run a different move. But in my opinion I think this build works well.