In completing the 1040ES, did you include the amount of future withholdings as payments as well? Also, any withholdings from your earnings?
Using joint income is the proper way, as you want to estimate what the tax bill will be for your filing status, presumably married filing joint.
Also, you might consider increasing your wife's withholding from her paycheck. That might eliminate the need for 1040Es entirely, if enough withholding is made from all sources.