Having been both to MP (a few years ago) and iquitos (last month on my 1M run) I'd recommend MP - much more impressive. We decided to go to IQT on the spur of the moment (and a little bit because the flights leave later) as we had already been to MP. Perhaps we took a bit of a chance with the health risks - but then I don't like "eating" malaria pills for five weeks to cover a two day visit - and after I have survived all the real indigenous food, I didn't worry too much.