From a lesser known uni, but very prestigious in my country - do I tell my referee to make this clear in my LOR for USA applications?
First of all, it is a tough position to be in as a student to have to give faculty advice on how to write your graduate school letter of recommendation.  To give them too much guidance may not be appropriate, and as someone who has not yet completed a PhD program or read or written any such letters, you almost certainly don't have the expertise do properly advise them either.  Thus I would urge you rather to seek out writers who have previous experience writing letters to North American universities.  One of the most important qualities of a top world university is that they regularly place their students at other top world universities, so (as @Tobias Kildetoft has pointed out in comment) I would expect there to be many faculty members in your department who have experience writing such letters.  I think it is much less awkward to try to choose letter writers based on this expertise than to try to give your letter writers letter writing advice.

But assuming the premise of the proposal: it is not clear to me exactly what information you are hoping to provide.  The world's top hundred universities are largely well known to each other, and moreover it is the responsibility of those who are evaluating your application to know or learn enough about your university in order to perform that evaluation.  When I do graduate admissions and get an application from an institution that I am not familiar with, I do spend time familiarizing myself with it.

In terms of rankings: Times Higher Education [a London based magazine] places twelve UK universities within the world's top hundred: Oxford (1), Cambridge (4), Imperial (8), University College London (15), London School of Economics (25), Edinburgh (27), King's College (36), Manchester (55), Bristol (71), Warwick (82), Glasgow (88), Durham (96).  It is reasonable to expect a reputable North American PhD program to have heard of all of these institutions.    Individual faculty members will also have their own opinions on the relative merits: for instance, in terms of the kind of mathematics that I do, I view Bristol as being very strong, perhaps at about the same level as Imperial.

If the faculty who process graduate admission do not agree that your institution is one of the world's most prestigious, simply pointing out that it is one of the top ones in the UK according to some metric may not change their mind.  They should instead offer concrete evidence of the excellence of their program, e.g. by talking about world-leading faculty members and former students who have been placed in other top institutions.