I'm about to start my second playthrough, this time i want to go down the route of a sniper. I'm stuck on where to put points into S.P.E.C.I.A.L for the most effective sniper build. Any help would be appreciated.

Just make sure your luck is 9. Pretty hard to screw up a sniper.

I'd go 5 5 6 1 4 9 9.

Agility

S: 6
P:7
E:5
C:1
I:7
A:7
L:7

Worked really well for me in FO3 and i carried it over to NV. Perspective and agility are a must with a little luck to back you up. Stealth (for critical bonuses),guns (obviously), and repair are good traits to focus on for FO snipers.

I play as sniper and didn't know that you must be strong to handle rifles. 5/6 for the standard high damage rifles, 6/8 for sniper rifles. Weapon handling perk gives a +2 bonus on lvl 16, so you need at least a basic strength of 6 to handle all weapons.

S 5 - you don't need more early on, later you will implant it to 6 - and maybe take weapon handling or power armor for big guns.
P 5 - again, implant to 6 before lvl 12 so you can get Better Criticals which is crucial for a sniper who sneak-crits with almost all attacks.
E 6-8 - you want plenty of implants here, also helps your other survival statistics. Don't think you won't need END being far from enemies.
C 1-5 - you don't really need to rely on companions so you can move points from here over to INT if you prefer.
I 7-9 - there is 1 skill point of difference per 2 levels of INT so there's no point going too crazy with it, depending on how much you want to lower your CHA. You are still aiming at 8-9 with an implant.
A 4-5 - perks based on this svck horribly because they are VATS-based, and you don't use VATS as a sniper due to low accuracy, you just snipe real-time which is 100% accurate
L 8 - Give it +1 Intense Training at lvl2, then implant to 10.

Make sure you have Trigger Discipline trait. Oh, and ignore all the VATS-based perks like Sniper, Hunter or Anatomy for example, they aren't for you. Take Finesse and Better Criticals, that's all you need.

Still, Sniper build is so overpowere you could as well go something like this and win:

S 1
P 10
E 1
C 10
I 1
A 10
L 1