In the Forgotten Ruins area up north are 9 altars on which you can put flowers. Putting flowers in certain patterns will unlock crates with stuff. In one such crate you should get the winged boots. I don't remember for sure but I think you can find hints to such patterns all over the game.
Spoilers:
According to the EBF fandom wiki, you can get the boots by placing flowers on all altars except the middle and lower middle one, in an inverted U shape.
