I'm 95% sure it was Annie. She had marco's ODM gear, and Marco's body was only partially destroyed. A normal titan would have eaten all of him, even if not in one bite (for example, carula jaeger) and if another soldier had killed it before it could eat the rest of him, there would have been a witness to Marco's death, which they didn't have. The last time we saw marco alive, he looked away from eren sealing the wall, and looked utterly shocked. (As if he saw something he wasn't supposed to) while Reiner and bertholdt's location at the time are unknown but Annie was definitely close to his location.