Snake has dodged smilair things, like the energy beam Metal Gear fires, two vulcan canons (which fires over 100 shots per half minute) and explosives, plus an assault rifle from point blank range. He could dodge it, especially if he is invisible, Samus suit and radar is disabled and she has MC firing at her as well. MC's cortana could hack into Samus suit, disabling the visor. Snake could toss a chaff which if anything would at least knock out the visor and the radar she has.
A stinger fired from Snake would indeed send Samus flying. It might not puncture through her suit instantly, but if it can make Metal Gear unsteady (it does when Fox fires), (A huge 10 thousand ton machine with unpenetratable armor) it would send Samus flying, maybe knock her out inside her suit....
I remember in Metroid Prime, where Samus isn't even HIT by the explosion, she jumps to her ship and the explosion of that station shakes her suit, and several parts FALL OFF her suit....