Generally, uniques have better stats than their common equivalents. So I'd go with the former.

The only downside to unique weapons is that they can't always be repaired with their common counterparts. But there are other ways to repair them.

Jury Rigging moment

The only downside to getting that perk is that you have to have 90 repair, so if you want it early level, you can’t work on any other skills

In FNV, they also usually can't be modified