Vinyl is hard to paint. Ideally, use a filler that matches the factory color. If you must paint, use a spray paint specifically formulated for plastic (like Krylon Fusion).
Some cracks signal a terminal condition. Replace the entire window sill immediately if you observe: cracks on window sill
Homeowners often dismiss a 1-inch crack as trivial. This is a costly miscalculation. A crack acts as a capillary bridge. Consider what enters that microscopic gap: Vinyl is hard to paint