I say get the 5.9. I bought one almost two years ago, an 2004.5, an immaculate one owner, with 136K at the time, that was used to tow a fifth wheel. Like you, our truck doesn't get driven a lot when not camping. We put about 5-7K per year on it, so it sits quite a bit. We have had NO problems at all with it, have literally only had to do maintenance, no repairs, and it is a great tower. I was lucky -- previous owner had put a Pacbrake on it, which works fantastically.
As for emissions, we live where our 5.9 has to be emission tested every year. I don't personally care if anyone does a delete, but I would be careful, as some areas that are not currently requiring emissions testing of these older trucks, may do so in the future.