In order to get the Ultra Boots, you have to:
1: Go to Toad Town Tunnels via OUTSIDE pipe, and go down the hole.
2:Go right and surf with Sushie to the other side of the "lake". Go through the door.
3:Take Lakilester and go over the spikes to the pipe on the other side.
4:Get to the other side of the "maze" while fending off the Spinys.
5:Go across the room with the Dark Koopas to the other door.
6:Go up onto the spring and across the wall. Open the chest and you have the Ultra Boots!
PS: To get Lakilester, you have to go to Flower Fields and then go to the Sun Tower using the path with the Bubble Plant. Go back after talking to the Sun. Lakilester will show up.Then you get to fight, and afterwards, keep Lakilester as a Party Member. He is the last Party Member to join your team.