Well I kind of go for the following:
S.P.E.C.I.A.L.:(Probably not the best possible for Sniper, but there other considerations!)
Strength: 6
Perception: 5 (see perks)
Endurance: 5
Charisma: 6
Intelligence: 6
Agility: 6
Luck: 6
Implants:Like Pokemon, got
buy get 'em all.
Starter Perks:Four eyes: To give a +1 perception for what I feel is the manadatory wearing of sunglasses.
Small Frame: For the +1 Agility, just watch out for mines!
Progression Perks:Intense Training: Points into Endurance, to make PC tougher and allow more implants, as well as Agility for Guns.
Bloody Mess: For +5% extra damage, as well as the gore.
Commando: For increased accuracy with two handed weapons.
Finesse: For the +5% Critical chance.
Sniper: For the increased chance of a successful head shot.
Better Criticals: For +50% damage for critical hits.
Weapon Handling: To use favourite gun (see below) without sacrificing to many points in Strength.
Grim Reaper's Sprint: For more V.A.T.S. head shots.
Skills:Guns: 100, for you know, using a gun properly.
Sneak: 100, for Sneak Criticals, plus a Sniper by nature isn't a hugely brazen affair.
Repair: 50 for making Repair kits, or 90 for Jury Riggin Perk.
Companions:Boone: For his Spotter Perk, making very long range Sniper targets readily identifiable. Also in completing his recruitment quest properly you get a nice beret giving you the usual hat +1 to Perception with an additional +5 Critical chance.
Rex: Mainly because I like having a dog, and he makes a good gun dog and will usually melee anything that's coming to smash your head in while you're scoped.
Weapon:Anti-Materiel Rifle: It's awesome, unsighted it makes quite a fabulous shotgun too.
Riot Shotgun: For when things get just too damn close.
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Probably far from perfect but it worked nicely enough for me and still leaves a fair bit of room for customisation in other areas, I was quite the Orator, Lockpicker & Explosives expert too.
Hope that is of some use to you