So i put 4 points to sneak perk and only left the disengage perk but my agility is 4. I want to be more stealthy if possible for melee kills. Should i dump more points into agility stat or it doesn't effect stealth at all?

Thanks.

I would it seems the S.P.E.C.I.A.L stats have more of a direct effect on how well the perks work which makes sense since they did away w/ the skills

Yes, AGI makes you better at stealth. Gives the perks a better base to work off of.