Per L&M Companion:
(d. 1696) Clerk in the Navy Office. He was appointed in 1663, and served in the Ticket Office c 1667-92, becoming chief clerk 1674-82 and 1689-92. In 1679 a man of these names was clerk to Sir R. Haddock in the Admiralty.
MR. A Nathaniel Whitfield of Gulford, Ct., initially and later worked as a 'clerk to the Navy Commissioners.' (various sources) If this is the same, the name Nathaniel crops up in various places in the extended Whitfield genealogy, this would have been his house before his return to England:
http://www.whitfieldmuseum.com/history.html . It was far from unusual for individuals and families to pass back and forth from New England in the C 17th., George Downing for one example http://www.pepysdiary.com/encyclopedia/106/
Chart showing the number of references in each month of the diary’s entries.