Deciding whether to use sill or seal with window depends on the context; both could potentially be correct.
A windowsill is the horizontal part at the bottom of a window's opening; it's like a shelf under a window.
A window-seal is what is used around the window to prevent air leakage; it keeps the uncomfortable cold or hot air from leaking in, and the comfortable cool or warm air from leaking out of the building.
DIY Network offers tips for How To Check And Seal Windows, the Department of Energy presents Tips: Sealing Air Leaks, and Reader's Digest offers 6 Tips For Starting A Windowsill Garden.