We know it is near Dufftown (Scotland), where Sirius Black is sighted, as is mentioned in
Hermione says “Dufftown? That’s not far from here!”
That’s the first clue. The second clue is there has to be a lake and a forest near the location, like we know so well from the story.
A thorough Google Maps search got me to this location, coordinates 57°23’17.6″N, 3°42’43.0″W. This place is 35 km to the west of Dufftown.
Attaching screenshots for your reference:
Update (1 November 2016):
Writer Bronwyn Johnson referenced my thoughts on Hogwarts’ location in a long Harry Potter series she’s been writing. You can find the chapter in question at the link below, if you want to skip straight to that part. Credit was given in the author’s note at the end of the chapter, so sweet of her.
Harry will be sneaking off later in the story to visit the nearest Muggle town – Grantown-on-Spey. In her words, she knew where to pick for her fic, based on my location for Hogwarts. The first in the series is “The Definition of Normal”, if you wish to check her work.