Fastest way to get data from a CSV in C++

Save in the file, how many numbers are written inside. Then, on loading resize the vectors. It could reduce the time a bit.

Of course your second version will be much faster - it merely reads the file into memory, without parsing the values in it. The equivalent of the first version using C-style I/O would be along the lines of

if (FILE *fp = fopen("data.csv", "r")) {
    while (fscanf(fp, "%d,%d,%d", &x, &y, &z) == 3) {
        xv.push_back(x);
        yv.push_back(y);
        zv.push_back(z);
    }
    fclose(fp);
}

which, for me, is about three times faster than the C++-style version. But a C++ version without the intermediate stringstream

while (file >> x >> c >> y >> c >> z) {
    xv.push_back(x);
    yv.push_back(y);
    zv.push_back(z);
}

is almost as fast.