You have a few options:
Make a one-time payment on the web.
Login to your account, go to Update Personal Information, One-time Payment and complete the form.
Mail a payment.
Make a payment at one of the E-ZPass® NY Customer Service locations
Do not use E-ZPass® until your account has been replenished. Take the tag out of the vehicle or place it in the "read prevention" bag. If you are a credit card customer, your account will be replenished whenever the account balance falls below the replenishment point.
Change your replenishment method to credit card to assure an adequate account balance.
At Port Authority Facilities if you drive through an E-ZPass® lane with no money in your account, the video enforcement system will capture your license plate, the Customer Service Center will issue a violation notice and you will be charged an administrative fee along with the cost of the toll.
At MTA Bridges and Tunnels Facilities you will get a red light and two white lights and the gate will not rise. You will be required to pay the full toll in cash, and may have to pay an administrative fee, and surrender your tag. You must follow the instructions of the Customer Service Center when you replenish an account that has run out of money.
At New York State Thruway facilities if you drive through an "E-ZPass® Only" lane with insufficient funds in your account, you will receive a violation notice in the mail, which will include an administrative fee per violation.
At the New York State Bridge Authority, in a "mixed mode" lane, a Red Light and "E-ZBAD" will be displayed.
At the Peace Bridge, if you drive through an "E-ZPass® only" lane or a mixed mode lane, a red light and "Call E-ZPass®" will be displayed.
NOTE: If you are in an "E-ZPass® Only" lane, the above will be displayed and the gate arm will not rise. In either a mixed-mode or "E-ZPass® Only" lane you will experience delays and be asked to pay full toll fare in cash. If you frequently use our lanes with an insufficient balance in your account, an administrative fee may be charged to your account.