Are uniques the best equipment in the lategame or will sets and random equip exceed the top unique equipment?
Legendary items (the Diablo 3 name for "uniques") have the potential to be the best items, because they can have the most slots for affixes. But now that legendary items use largely random affixes as well, it is much easier for a rare or even magic item to be "better" because the couple affixes that it generated are worth more than all of the affixes that were generated on the legendary item.
Set items are legendary items as well, so again, they have the potential to be the best (since you also get the set bonus along with all the random affixes), but it will largely depend on which random affixes they get.
Legendary items are NOT meant to be the best gear in the game. Rare items are meant to be the best items in the game but they take a lot longer to find the best rare item for your class. The reasoning behind rare items being better than legendary items is that rare items have the potential to role out perfect stats.
Certain legendary items can have mods that cannot appear on rare items in that same equipment slot, thus making them 'better' depending on character build.
For instance, Andarial's Visage (helm) always has increased attack speed and critical hit chance where rare helmets cannot have these mods. This makes it highly desirable for classes who want to max out their IAS (such as certain demon hunter builds).
I would say that certain legendaries are indeed the 'best' equipment due to these unique mods.