Lemur866, that may be because right now many of the ruling elite in PR are not independentistas. I’m not saying that it will change with independence, but there is also the belief that it could not get any worse than it already is.
Is that a pound avoirdupois of salt, a pound Troy of salt, or £1.00 worth of salt? 
(a) Just to add: and none of us is happy with having to settle for “not get any worse”, bit the choices we get are just hopeless.
(b) Putting aside the very real corruption problem for a moment… part of those “high labor costs” take the form of US minimum wage laws and PR labor-protection laws. Since proposing to the people that they give that up is a pretty fast track to getting thrown into San Juan Bay, the new government would not be able to do too much about that part of labor costs.
© ahem abut the “ruling elite”: The people and organizations that dominate business, industry, the professions, trade, culture and every educational institution right now… will be the same the day after independence. They will still have a lock on the power structure. The clean-up has to start now, not then.
JRD, I don’t disagree with C, I’m just saying the reason people may think corruption at least the one that takes place in the places you’ve indicated will decrease, or at least not get any worse (which is not better).
Once PR is independent,(and the spigot from Uncle Sam is turned off), agriculture and business on the island will have to adapt. Since the artificial subsidies from the US will end, the costs of local production will drop, and PR will be able to employ local people to farm, produce things, etc. The hugely corrupt school system (which squanders most of the money from the US) will have to adapt-they will cease paying bribes to the local politicians, because the money will no longer be there!
In short, there will be a few bad years following independence, but later on, the quality oflife will vastly improve for the people of PR.