Kelly's 1855 Kent directory shows:-
Salem Chapel, aka Congregational Baptist Chapel, Particular Baptists, Biggin Street; built 1840; minister the Revd Frederick Russell.
Unitarian Baptist Chapel, Adrian St; built 1820 on a site dating from 1643; minister Revd Thomas Barker Wawne Briggs.
Baptist Chapel, Commercial Quay; minister Revd John P Edgecombe.
No mention of St Mary's, other than the Church of England in Cannon St. It is unusual, though not unknown, for nonconformist Churches to be named after saints. Could it be a misreading of "Salem"? Or maybe "St Mary, (Baptist)" is just a way of saying that these names were recorded in the CofE registers.