The difference is Usage. That and the path to sniper school. I've worked with S/S from 3/2 and their were a few in my company along w/ some guys fom recon.
Now from what I've gotten fr/ them was, for one the basics, Recon Snipers support Reconnaissance Ops and SS support MAGTF Ground Ops (usually but not limited to INF Ops).
They both attend the same schools SS Basic(10.8wks) and most the 4wk Pre-Sniper course. Both are called Scout-Sniper. What makes a Marine Sniper a Scout-Sniper is the added emphasis on training and usage as a Forward Observer, which gives the SS more latittude and freedom of movement.
INF SS: Just to add to what TRex has said when I worked w/ 3/2, in the summer of '03, in the INF BN there is a SS Plt of about 36 men and within the SS Plt is the 16 man STA section. Now from what they told me is they only form up a 16 man STA for MEU(SOC) Deployments and its from within SS Plt.
They give the Marines selected for STA additional training and were attached to the Reconnaissance and Surveillance(R&S) section of the former MSPF, giving them the latitude of Force Recon S/S.
But that doesn't mean that INF SS don't do cool Sh*t, Marine INF S/S still have more freedom then almost any other Infantry sniper whether conventional Infantry or specialized Infantry.
I think the coolest thing that I had ever seen was when I was on Haditha Dam w/ Small Craft working w/ 3/4. Their SS had confiscated civilian vehicles. Dressed as Iraqi civilians they cut holes in the trunk and removed the back seats driving around engaging targets w/ the shooter laying in the trunk and the driver/spotter selecting the targets.
RECON SS: Recon SS are usually a little older than INF SS b/c they usually have to be a proven operator in Reconnaissance unit B4 being sent to any SS schools. There is a T/O for at least 1 SS per 6man Recon team but there are usually 2 per team and 3 teams per Recon Plt.
Recon SS support recon missions; if they are BN Recon support missions out to the Distant Battle Space, if Force they support in the Deep Battle Space. Dist Batt SP are missions about 10 to 20 miles beyond the Foward Edge of Battle, Deep Batt SP is basically all missions beyond Dist BS.
Some basic missions range fr/ 2 man missions to engage targets or simply detaching fr/ the Team while on assignment to provide overwatch while on Recon missions or complex urban ops. It also gives the 6man team the option of engaging targets of opportunity should they arise.