You seem to be expecting Matlab to read an EPS file written by Mathematica and to further manipulate it. Since an EPS (Encapsulated PostScript) file will contain only a 2D projection of your 3D plot, one intended for printing, even if Matlab will read and display an EPS file it isn't going to be able to do anything with the 3rd dimension which isn't directly represented in the file. I think this is where you are going wrong.
Surely what you ought to be doing is exporting the datasets from Mathematica and importing them into Matlab ? If so, edit your question and provide some more details about your datasets and the code you've written so far.
I'm a little surprised that you expect Matlab to be able to display large datasets with significantly more performance than Mathematica, it's not something I've noticed but then it's not something I've looked closely into.