There was no symbol that represented Estonia at this time, since heraldry hadn't spread there yet. Not long after Denmark took over Tallinn, the city started using the three blue lions on gold from the Danish coat of arms. After Sweden took over in the sixteenth century the city's coat of arms became associated with the whole country. I'd say that's the earliest thing we can genuinely call a "symbol of Estonia".

It's also worth pointing out that the Danish flag probably didn't exist in 1219, heaven-sent or not. The earliest evidence we have for it comes from the 14th century, and that flag looks very different from the modern Nordic cross.