Well if you want to take overall quality that still doesn't give NYY an obvious advantage. John Sickels, an authority on milb prospects, ranks Ellsbury an A-, Lowrie an A-, and Masterson a B. Only Marquez is ranked for NYY (as he is the only minor leaguer in their offer) and is ranked a C+. So assuming Hughes is an A (his ranking last year) and Cabrera a B, the two packages consist of A-, A-, B and A, B, C+. That doesn't look like one offer is clearly better than the other in terms of overall quality. Even if you deem Cabrera as only a "little drop off" from Ellsbury and give him a B+, the packages are still pretty even.
Baseball Prospectus ranks Ellsbury a 5 star player, and Lowrie and Masterson 4 star players. Marquez isn't on the list of top 11 NYY prospects, but the list ends with 2 star prospects so I'll give him that. If Hughes is a 5-star and Cabrera a 4-star (a stretch), then they would deem Bostons offer superior to NYYs (5,4,4 > 5,4,2).
I know you disagree, but one of the most respected milb talent evaluators and one of the most respected baseball analysis sites says that the two packages are very comparable.