Watch the vid that Waki has posted. The bosses take more damage if they are hit by falling rainbows. So if you have more than one rainbow, 'park' them repeatedly in the air, wait till the boss is in range and jump under the rainbows so that they drop on him. If you have 3 rainbows, park them in the air 3 times at the same place and drop them on the boss, that will almost kill him.
If you only have one rainbow, run to one side, turn around, wait for the boss, jump-shoot a rainbow at him, run to the other side, rinse and repeat.