Hi Subham!!! There are only 4 banks which are authorized to issues E-SBTR which are as follows Bank Of Maharashtra, Canara Bank, IDBI Bank and Punjab National Bank.
But remember, you can not make only registration fee through E-SBTR. (You can pay only registration fee through simple receipt only)
Your welcum Shubham!!! The Registration and Stamp Department has provided various online modes to pay the Stamp Duty and Registration Fee through Internet Banking, Debit Card, Simple Receipts and ESBTR.
And you can also make payment through GRAS (Government Receipt Accounting System) Finance Department (FD) Government of Maharshtra through the website: https://gras.mahakosh.gov.in/echallan/
Yes, you can pay the Stamp Duty and Registration Charges online in Thane. Registration and Stamp Department has authorized limited banks that can collect those charges through internet banking which are as follows; Andhra Bank, Bank Of Maharashtra, Bank Of Baroda, Bank Of India, Canara Bank, Central Bank Of India, Corporation Bank, Dena Bank, IDBI Bank, Indian Bank, Indian Overseas Bank, Punjab National Bank, State Bank Of Hyderabad, State Bank of India, State Bank Of Patyala, Union Bank and Vijya Bank.