You always have to consider what the zwitterion is: it's a condition where an amino acid shows no net charge. You can think of it as a state in between
a mono-cationic and a mono-anionic form.
Whenever you have more than two pKa-values, you have to work out what condition they represent. For example, aspartic acid has 2.1, 3.9 and 9.8 as pKa values.
The first one 'represent' the cation: 1 net positive charge.
The second one is owed to the presence of 1 net negative charge.
The third is because of a possible second negative charge.
Now, going back to what I said in the beginning, you have to find where your zwitterion is. The answer is, of course, between pKa1 and pKa2:
pI = (pK1 + pKa2) / 2
in this example.