A wit is an exceptionally clever and perceptive person who often makes clever and perceptive statements that are amusing (Random House Dictionary). One reason why we can see Maria being characterized as a wit in Act 1, Scene 3 is because she frequently makes puns, or plays on words.
One example of a pun can be seen when she and Sir Toby are discussing Sir Andrew's merits or lack of merits as a suitor for Olivia. Maria argues that Sir Andrew is an absolute wasteful fool. But Sir Toby argues that Sir Andrew has merit because he can play a musical instrument, fluently speak four different languages, and "hath all the good gifts of nature," apparently meaning that Sir Andrew is handsome (I.iii.23-25). Maria uses a pun in her retort, "He hath indeed, almost natural" (26). In Shakespeare's time, the word natural was also a slang term used to mean idiot (eNotes). Hence, what Maria is wittily saying here is that Sir Andrew certainly does have all of the gifts of nature: He was blessed by nature and naturally made an idiot. Hence, since we see that Maria is cleverly able to make puns, she is most definitely being characterized by Shakespeare as a wit.