Bigger cities normally have lower AVG income for many reasons. One you might want to look at is your Sims AVG age. Since people under 15-16 normally would not be working. Also look at your unemployment chart. If a lot people are out of work then the AVG income will just keep dropping.
Example:
City size of 250,000
Work force 222,500
Unemployed 27,500
Work force AVG income of $65,000
A scenario like that would make the AVG income $57,850
A small drop but a drop none the less. But it's a good example how a lot of things affect the AVG income.