Would I be receiving a cheque if I owe Canada Revenue Agency?
I found an answer at Canada Revenue Agency that addresses this directly. Quote:
24. I have an outstanding debt with the CRA and didn't receive my GST credit because I owed money to the government. Will I receive my OSTTB payment?
Yes. The OSTTB payment cannot be applied against other debts, such as outstanding income tax payable. If you are entitled to an OSTTB payment, you will receive it.
However, if you are reassessed and it is found that you received a payment that you were not entitled to receive, or you received more than you were entitled to receive, you must pay back that amount or the amount will be deducted from future entitlements.
Similarly, if you are reassessed and it is found that you received a lower payment than you are entitled to receive, you would be issued the additional amount.