I think it would be a mistake to assume that yonder generally represents a greater distance from the speaker than there does. Either term, unadorned, is ambiguous as to distance. The key to conveying a sense of how distant a thing "there" or "yonder" actually is lies in the modifier or modifiers attached to it, although some resulting phrases (such as "over there" and "over yonder") remain exceedingly vague as to distance. Consider, for example, the popular World War I song "Over There" by George M. Cohan, where there referred to "in Europe"—that is, across the Atlantic Ocean.
Because many people today do not use yonder as a standard part of their vocabulary, they may associate it with a particular usage that implies considerable distance, as in the song "Way Down Yonder in New Orleans." But for people who use yonder regularly, I suspect, the range of distances that the term can comfortably comprehend is quite broad. My grandfather, who was born in western Kentucky in 1903, used yonder occasionally and variably, often to indicate an indefinite place—for example, "the cows are grazing out yonder," meaning that the cows are grazing in a nearby pasture but it isn't entirely clear which pasture or which part of a single pasture they are in.
You can get a sense of the range of use of yonder in everyday speech in regions where the word was common by looking at recorded examples of its use (in the sense of "there; at or in that place") in Harold Wentworth, American Dialect Dictionary (1944):
'Yonder it is, Squire' [1871, Georgia]
'It [the river] rises yander' [1881 Tennessee]
'a-standin' out yander' [1888, Georgia]
'The road is back yander' [1895, Kentucky, Tennessee, North Carolina]
'You must do this or go down yander, one!' [1902, Illinois]
Denotes a long distance & an uncertain direction. 'His folks live back yander,' meaning no particular direction or distance. 'I heerd he was going back yander where he came from.' [1903, Missouri]
Extremely common in 'over yonder' [1905, Arkansas]
'[a]way yonder' = far [1906–9, Arkansas]
A noun used with a preposition to express a specified place. 'In yonder,' = in the place specified. 'Over yonder' refers often to the future life. 'Look ayonder.' [1908, Alabama, Georgia]
'It's yunder over in the corner' [1909 Massachusetts]
'That's my gat down yonder.' [1911, Massachusetts]
'It is in yonder' [1915, West Virginia]
'See that tree over yender?' [1917, Ohio]
'Out yonder' and 'The woods back yonder' [1917, Vermont, New York; 1920, North Carolina]
'He went yander right now!' = disappeared in haste [1923, Missouri]
'He is down yander' [1925, West Virginia]
'I got another pipe yonder home ... away down yonder in dem thickest pine woods ... a-sleepin right yonder on de bed ... Youcould stay yonder to school ... de boat yonder on de river ... I ain' got a stick of wood yonder home' [1928 South Carolina]
'Looky yonder' = Look there. Used of any small or great distance. [1930s, West Virginia]
'Over yonder on the grinsad.' [1930, Maine]
'that hollow back yander' [1936, Kentucky]
'round yonder back of that piney pint' [1937, Kentucky]
'There he goes! Yander, see 'im!' [1938, Kentucky]
'Gone too fur yonder' [1938, Florida]
'Look yonder ... sitting right up yonder ahead of me ... Look a-yonder [1940, Gulf of Mexico states]
'over yonder ... is where it ends ... from here to yonder' [1940, Mississippi]
'Yonder comes Ced ... Look comin' up the street yonder' [1940, Arkansas]
'that beech grove down yander' [1941, Kentucky]
'Yonder atop the roof' [1941, West Virginia]
Wentworth selected these examples mainly to show variants in pronunciation, prepositional use, and regional distribution of yonder; but the examples also convey a sense of how broadly applicable yonder was to different situations for speakers who used the term frequently. For some of them, at least, yonder seems coextensive with there as a term for position or distance. Such speakers might at times use yonder in connection with distant locations, but they might also use it in reference to the corner of a room they were sitting in, for example, or a bed elsewhere in the same house.
The decisive factor in defining how distant yonder is for a particular speaker, in other words, is whether the speaker uses the word frequently and widely in situations where other speakers might use there, or whether the speaker uses it relatively rarely and in particular contexts—for example, as part of a longer set phrase such as "way over yonder."