For one thing, Maria sees both Sir Toby and Sir Andrew as being two peas from the same pod, meaning similar in character, or lack of character. She sees them both as being drunken, extravagant, wasteful fools.
We see her calling Sir Andrew an idiot in the line, "He hath indeed [all the good gifts of nature], almost natural" (I.iii.26). In this line the word natural has a double meaning because it was used in Shakespeare's days as a slang term to refer to an idiot (eNotes). She further goes on to describe that he is an idiot because he is both quarrelsome and antithetically a coward. He hasn't the guts to defend himself once he has started a fight, which is very foolish and idiotic.
When Sir Andrew enters the scene, she proves how idiotic he is by making fun of him with word plays that he does not have the sense to understand. One example is that she calls him impotent by shaking his hand and making a pun out of the word dry. As the editors of eNotes explain, "In Shakespeare's time, a person with a dry hand was believed to be impotent" (eNotes, 67).