This would include the 2008 "Brainiac" story, which led directly into New Krypton with Pa Kent's funeral. Both of these stories came out at exactly the same time, and unlike Batman, don't seem to tie in to each other at all... so which comes first or when in the chronology? The problem is we have a bit of a contradiction or paradox in that Bruce Wayne shows up at Jonathan's funeral when he already perished in Final Crisis... and yet Pa shows up in one of the FC tie-ins.
I guess if you really, really want to force it you could say that it was Dick at the funeral from afar, or that Crisis takes place in the week between when Pa dies and they bury him, but there doesn't really seem to be a satisfactory answer other than "they didn't think about it." It also doesn't help that Superman takes off for New Krypton right after that story, and the Daily Planet building is destroyed in FC. If I had to pick I guess I would say New Krypton takes place after since Superman becomes so preoccupied with Kandor's enlargement to the exclusion of all else, and we overlook Bruce's one panel cameo at the funeral, but there was just no level of coordination in the way that Morrison tied Batman RIP into the crossover so seamlessly even if that didn't please anyone.