There's a version of the Bresenham algorithm for drawing circles. Consider the two dimensional place at z=0 (assume the sphere is at 0,0,0 for now), and look at only the x-y plane of grid points. Starting at x= R, y=0, follow the Bresenham algorithm up to y = y_R, x=0, except instead of drawing, you just use the result to know that all grid points with lower x coordinates are inside the circle, down to x=x_center. Put those in a list, count them or otherwise make note of. When done with two dimensional problem, repeat with varying z and using a reduced radius R(z) = sqrt(R^2-z^2) in place of R, until z=R.
If the sphere center is indeed located on a grid point, you know that every grid point inside or outside the right half of the sphere has a mirror partner on the left side, and likewise top/bottom, so you can do half the counting/listing per dimension. You can also save time running Bresenham only to the 45 degree line, because any x,y point relative to the center has a partner y,x. If the sphere can be anywhere, you will have to compute results for each octant.