I know there are some nominally religious people who might visit some popular pigrimage site just because they want to look around and take photos and that kind of blurs the line between the two, but the pilgrims who go to Mecca I don't see as ambiguous at all. Personally, I would definitely not count them as tourists. They're not on a tour. They're not sightseeing. They are performing a highly ritualized and specific prescribed religious duty.
As predicted, the numbers blow away most of these cities. For example, San Diego, #10 on the list, receives 29.6 million visitors annually. Quite a bit more than Prague's piddly 3.7 million (plus whatever it gets from domestic tourism; maybe another 100,000 or so?). I couldn't find consistent data (or in many cases any data) on most other world cities, but I read something somewhere that said Shanghai received 70 million visitors to the world expo they had there last year. They're predicting something to the tune of 3 billion domestic tourists in China this year. Not counting them simply because they aren't crossing any borders makes it very hard to see the real picture clearly. Thanks for the inspiration! :)