so a little back story: i originally played ME1 and 2 on 360. i recently let my Live subscription run out and plan on buying ME2 on Steam before 3 hits, and i already have ME1 on Steam. 
 
so now my question is if i buy a physical copy of ME3 from Gamestop, i work there so i can get a discount....i know i know, i suck, but will my Steam save data still work with the physical copy? or am i gonna have to buy it through Steam? 
 
big ups for any help.

Yes they will work. The save files aren't different depending on where you buy the game, they all go into the same folder and are formatted the same. 
Since the game isn't out there isn't a 100% guarantee that it will work, but it did for the previous games and for pretty much every Steam game out there. Unless they go out of their way to prevent it they will work.