Depends...
I like to pick flying however it means it is just like walking around but in the air which means if I were to travel, I can only carry so much which in turn still limits me somewhat. To top it off, I can already fly as is (student pilot close to private pilot) and flying commercial is not too bad. Though I do like the absolute freedom being able to superman my way through any part of the world.
Invisibility.... Other than the obvious bewbie access, think of the covert advantages! You can easily sneek a peek into high security areas, divulge into $$$ secrets, secure access points to yourself, hell even fly for free by sneaking around (unless you are carrying something metal then it may look suspicious).
Now lets look at the consequences....
If everyone had the ability to pick of the two and own that ability then there could be problems. For flying, just imagine what problems of traffic we have on the ground as is and take it in three dimensions. And especially since we are going at 1000mph (is that ground speed?) then we will have people mess in the air. Not to mention there is the weather. You probably wont want to fly into a cloud and be in an embedded thunderstorm or freeze your butt off.
If everyone can have invisibility, then there would be countermeasures to invisibility and there are already stuff out there to detect people by (heat sensing) and people can still feel you or you can risk bumping into people and reveal your cover.
So if you were to give me invisibility, I'd take it if I can turn off at will any identifying signature that can be detected. With flight, give me the ability to carry a good amount of items and a way to fend off any bogeys in my way plus make me weather proof.
But if you want the simple answer, I pick flight!