I spoke to a CRA agent.

We can still mail in a cheque for the amount under $10,000.  If it’s $10K and more, CRA wants electronic payment or subject to penalty.

CRA online service does not have a feature to create remittance form for T3 payment as of now.  

Another way of paying the balance is to make payment to a deceased SIN (T1), and call CRA to transfer the funds from T1 to T3.