It feels really awkward. Manchester United are 16th and Tottenham are 17th in the PL. But they are playing against each other in the EL finale. One of the weirdest scenarios ever. 
You are right. The two teams that qualified for the Europa League final are at the bottom of the Premier League table. We have never seen such a scene before. Another important thing is that these two teams have not won any of their last 5 Premier League matches. In fact, both teams have lost four of their last 5 matches. Their performances are similar.
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But anyways... IMHO, Amorim's club is closer to the trophy. Why? Because Manchester United have a much better history in European competitions. This is my reasoning. I'm open for being surprised by Tottenham also but this is my thinking.
Manchester United is ahead in every aspect. Manchester United's squad is stronger than Tottenham's. Also, Amorim is quite good as a coach. I would even say that Manchester United has qualified for the Europa League final due to Amorim's sole efforts. And Amorim wants to win the title by any means. I want to rely on Amorim. I wish Manchester United victory.
I agree with you, finals are always difficult and unpredictable matches. Although Tottenham and Manchester utd are pretty bad in the league, in the Europa League they have given their best performances so far, so I think it will be a pretty balanced match.
As luck would have it for them they are already safe from relegation in the league, we could see something more epic