First, the bulk of the Frey and Lannister forces are at Riverrun, so it makes sense to have the wedding there since the guests (and the groom) are already there.
Second, it’s where our POVs are. Brienne went to Riverrun to get Jaime, and that’s where they both disappeared from.
Third, it works better thematically. We’ve already had the Red Wedding at the Twins, repeating it there retreads the same ground. But having Lady Stoneheart commit a similar atrocity at Riverrun – a place that’s been associated throughout the series as a place of safety, a place where family is protected and loved – complicates our understanding of revenge. If the cost of revenge is that this place is defiled, is it worth pursuing?