Dealing with uncertainty when reviewing a paper I agreed to review a paper that falls within my area of expertise. However, I am not particularly familiar with one of the techniques used by the authors.  On detailed reading, their use of this technique feels wrong to me, but I am by no means certain. It is not a method that I have seen applied before in similar contexts. I can't put my finger on a definite flaw, but it just doesn't quite seem to "add up".

Given my uncertainty, how should I comment on this in my review? I have the option of simply stating “I cannot comment on the validity of [one particular aspect of the methodology] as it is outside my area of expertise.” Alternatively, I could raise my concerns, while making my uncertainty clear, but would this undermine confidence in my review overall? Is it unfair on the authors to raise an objection on the basis of my incomplete understanding?
Yes, it is fair to raise concerns when you don't understand a paper. It is the authors' job to explain in enough detail what they did. Especially if the method used is uncommon, then it needs to be justified. That justification needs to be done in a way that it is understood by the intended audience, not just the specialist within that audience. 

Tell the authors in as much detail as possible why you think their method does not feel right. Maybe the method is problematic, and they will appreciate that feedback. Maybe they did not explain their method well enough, and they can use that feedback to pinpoint what was not clear.