Acrylic paint, when dry, is waterproof
Chances are it isn't the glue you used, but the fact that your gluing not-terribly-flexible vinyl to a shoe. shoes flex. Often the key to getting good adhesion on silicone or latex materials is pressure. Putting tight clamps on the things being glued together can go a long way in how well the bond holds up. In this case, it's rather challenging.
Try stuffing the shoe with paper really, really tightly. Glue the top on. Then wrap strips of fabric around the glued portion of the shoe as tightly as you can. Let sit for at least 4 hours.