When did ‘wherry’ become ‘ferry’?
It never did. A wherry is a type of boat – usually characterised by having a deck, often oars and a particular lay-out of sails where fitted. Compare, skiff, cobble, yacht, cutter, barge, etc.
The boats crossing the Thames before all the bridges were built in the late 1700s were called wherries.
This is simply not true. Wherries existed throughout the UK from the early 15th century after the design had been created.
Ferries existed throughout the UK from pre-Roman times. Not all ferries were wherries and not all wherries were ferries.
Wiktionary; however, says the term wherry is much older:
No it doesn’t. Ferry existed in Old English.
Meanwhile, Etymonline says the origin of ferry–meaning a boat for transporting passengers and goods, can only be traced back to the 1580s.
No. It can be traced back to Danish and Swedish and other Germanic languages and appears in Old English. (see etymology below)
Today, we're all familiar with the term ferry (ngram), which is also a verb. Clearly it has always been more popular.
This is nonsense. It is rather like saying “Today, we're all familiar with the term rein, which is also a verb. Clearly it has always been more popular than “checkpiece”.”
The need to refer to a ferry was always greater with the public than the need to refer to a wherry.
but what is the history of wherry
You have already give one possible origin of “wherry”, you have therefore given your own answer.
Etymology: Etymology obscure; perhaps < whirr n. with suggestion of rapid movement.
The OED states
A light rowing-boat used chiefly on rivers to carry passengers and goods.
1443 For. Acc. 21 Hen. VI G dorso (P.R.O.) Vnius Batelle vocate Whery.
A large boat of the barge kind: see quots. local.
1589 R. Lane in R. Hakluyt Princ. Navigations iii. 740 I tooke a resolution with my selfe..to enter presently so farre into that Riuer with two double whirries, and fourtie persons one or other.
C1. wherry-boat n. 1538 A. Fitzherbert Newe Bk. Justyces Peas 134 Passynge the riuers of Thames or Medwaye by barge or wheribote.
and why is it virtually unknown nowadays?
Because wherries are not popular nowadays and thus there is little need to refer to them.
Ferry: - We first have the verb:
Etymology: Cognate with or formed similarly to Old Saxon ferian to sail, to travel (Middle Low German vēren to cross a river or other stretch of water by means of a boat), Old High German ferien , ferren to cross a river or other stretch of water by means of a boat, to convey or transport (people or goods) by ferry boat, to sail, navigate, or direct the course of (a vessel)
†I. Senses relating to the general action of conveying or transporting.
- a. transitive. To carry, convey, or transport from one place to another. Obsolete.
OE Beowulf (2008) 333 Hwanon ferigeað ge fætte scyldas?
Then the occupational and vessel as a noun.
- A boat or ship used to carry passengers, vehicles, or goods across a river, relatively short sea crossing, etc., esp. as part of a regular service; = ferry boat n.Recorded earliest in ferryman n. (as a surname).
1192 in Publ. Pipe Roll Soc. (1926) II. 278 Robertus ferriman.
1290 in M. T. Löfvenberg Contrib. Middle Eng. Lexicogr. & Etymol. (1946) 88 (MED) [A boat called] Le ferye.