The first thing I would say is that I don't think we are good enough to be picky about which cup we win. If someone offered me two LC wins every five years I would be more than happy.
Having said that to answer your question in the mythical world of free choice I would choose the SC for two reasons. Firstly for what little it is worth it gets us into a later round in Europa League versus finishing second/third in league and secondly it is seen as a more prestigious cup (plus having been lucky enough to have seen us win 5 Scottish Cups and 3 League Cups first hand there is something about winning the SC standing in short sleeves versus LC with 17 layers of clothes on!!!)