How to determine what an attributive clause modifies

While attributive clauses don't always modify the immediately previous noun, that is the default assumption, as the other answer says. If this reading produces nonsense, the attributive clause can be assumed to modify something else.

As written:

It has been associated with neoclassical economics and with the neoclassical synthesis, which combines neoclassical methods and Keynesian-approach macroeconomics.

the attributive clause modifies neoclassical synthesis. Removing the second with would not change this.

To make it modify neoclassical economics and the neoclassical synthesis, you need to change the verb from singular to plural. In this case, the sentence reads better without the second with:

It has been associated with neoclassical economics and the neoclassical synthesis, which combine neoclassical methods and Keynesian-approach macroeconomics.

To make an attributive clause modify "It", you need to rewrite the sentence.

This technique, which combines neoclassical methods and Keynesian-approach macroeconomics, has been associated with neoclassical economics and with the neoclassical synthesis.

(where the appropriate noun should be inserted instead of technique, which is my best guess at what "It" refers to.)

Finally, Keynesian-approach needs to be hyphenated, because it's a phrase being used as an adjective.

I think normally the attributive clause (which combines...) modifies the immediately preceding term. Which in this case is the neoclassical synthesis.

Personally I believe the comma is misplaced, and that's why OP has trouble parsing the sentence. I'd have written something like...

It has been associated with neoclassical economics, and with the neoclassical synthesis (which combines neoclassical methods and Keynesian approach macroeconomics).

Note that I'm making this interpretation on the basis of normal grammar and common sense only. I don't actually know what the neoclassical synthesis actually means. If in fact it doesn't mean what I've put in brackets, the alternative interpretation is that it's those two associations (neoclassical economics and the neoclassical synthesis) which do the combining. In which case the attributive clause modifies the entirety of the preceding text (and the comma is correctly positioned).

I'll also just point out that by strict grammatical rules I think only that second interpretation is valid. It's just that I'm sceptical as to whether it makes sense - which is why I've assumed the comma is misplaced, so I can have a different reading which seems meaningful to me. Anyone who knows what on earth the neoclassical synthesis means in economic theory may wish to correct me on that point.

LATER: It's easier to analyse the sentence structure without these abstruse technical terms. So let's replace them with two sets of simpler words...

It's associated with chalk and cheese, which combines milk and bacteria.

It's associated with chalk and cheese, which combines mining and farming.

Having just gone to the trouble of looking up the neoclassical synthesis, I believe the term does match the bracketed definition in my earlier suggested alternative. Therefore it corresponds to the first of my 'simplified' versions above, which I would recast as...

It's associated with chalk, and cheese (which combines milk and bacteria).

...although in this simplified version the comma may be considered unnecessary because the reader doesn't really need to 'pause for breath', and the correct reading is probably obvious anyway.