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The submarine can be skipped by doing the tongue glitch in this level. To perform the trick, you first need either a pow block, or a big egg. Big eggs are recommended as there is no known way to consistently get a POW block. See below for setups on keeping big eggs from 2-7 into 3-3.
How to 3-3 submarine skip
In the 2nd screen of 3-3 with a big egg, grab an enemy, throw the big egg into the air, and spit out the enemy right before the big egg lands. This will activate the tongue glitch.
Yoshi's Island Speed Run 3-3 any%