Like you, I consider myself lucky enough to have seen both players, although obviously it was harder to watch Napoli in the mid eighties so didn't see anywhere near as much of Maradona's career as I have Messi's.
I think you have to balance out things like the pitches and the way a skilful player could be hacked about, with the sheer level of physical, tactical, mental superiority of modern football that Messi has had to play in, and lets not pretend Messi hasn't been subjected to a barrage of physical punishment too.
I'm not outraged that people would choose Maradona, I can understand why, it's hard to compare players from different eras, and these two are very comparable, and have very similar skill sets to compare, unlike the comparisons with people like Pele and Cruyff etc, who were totally different players.
And they both did it in what was the best/toughest league in Europe at their time (or at least for phases of their careers in Italy and Spain anyway). People will argue Messi got to play in a side with Iniesta, managed by Guardiola, but lets not ignore he continued to perform and produce amazing levels after both of those had gone.
Maybe one of the advantages Messi has given himself is that his private life has been stable and that has allowed a level of focused professionalism that enabled him to produce much more and much more consistently, I don't know, we'll never know the true impact of Maradona's private life had on his performances and output (although we've got a fair idea), but having seen both, and loved both, it's Messi for me, all day long.