There will be no significant difference, however:
Installing packages from Ubuntu repository in some cases is safer and solid, because you stick with something that was well tested for your distribution, before being distributed. It will be also properly handled during dist-upgrades.
On the other hand, if nginx itself has its own repository, suited for your distribution, it's worth going with it, as you'll get the most up-to-date version of the software.
Which method is recommended
It's always recommended to use official Ubuntu repositories when it's possible. Any custom repository may cause problems or incompatibilities at some point. However in this case I think it's fairly safe to stick with PPA. I believie folks behind nginx know what they're doing :)