Geoff Minns on 4 Sept., 2011 reported that he had very kindly gone to the Bancroft Library and checked the St. Mary's burial records for 13 June, 1666, and for a week either side of that date.
There is no record of a burial of Sir Christopher Myngs in that period.
He suggested that Myngs' funeral could have been at St. Katherine's by the Tower, but he hadn't checked their records. This would be an easy walking distance of Seething Lane.
There's a lot of information about St. Mary's, Whitechapel, in the annotations on the date linked here.