Your choices are between doing it the RIGHT way and doing it the EASY way.
If you want to do the job properly, install the FLOOR FIRST. Makes all your heights proper, and you'll run into less problems down the road.
If you want to save money, or if you already have base cabinets and you don't want to remove them and reinstall them, then install your floor around them. However you may run into problems down the road, and you'll be wondering why your counter-tops feel too low all of a sudden. Also, with the amount of extra time you'll spend cutting around and trimming all the extra edges, you may find yourself wishing you had taken them out in the first place, and that the "easy" way wasn't so easy after all.
It's much simpler to install a floor in a square, open room, than one with finished pieces already installed. (and therefore the end result will look better too). As with any construction project, start with the bottom, and work your way up.