Very easy. Just call bwlabel on A
[labeledImage, numRegions] = bwlabel(A);
where A is a binary image.
Then use find() and pdist2() (stats toolbox) on B to get distances and select the smallest non-zero distance - trivial, but let me know if you can't do it.
Then, for your two pixels locations in B you want to check on, simply check if the labels are the same or different.
if labeledImage(row1, col1) == labeledImage(row2, col2)