From Arduino Uno R3 docs:
Vin: The input voltage to the Arduino/Genuino board when it's using an external power source (as opposed to 5 volts from the USB connection or other regulated power source). You can supply voltage through this pin, or, if supplying voltage via the power jack, access it through this pin.
5V: This pin outputs a regulated 5V from the regulator on the board. The board can be supplied with power either from the DC power jack (7 - 12V), the USB connector (5V), or the VIN pin of the board (7-12V). Supplying voltage via the 5V or 3.3V pins bypasses the regulator, and can damage your board. We don't advise it.
The Vin has a fixed voltage drop of 2V so to use Vin you would need a minimum of 7V.
While not recommend by arduino, If you know what you are doing have a clean 5V and you don't connect it backwards it will not matter that you bypass their regulators and connect it directly to the 5V pin. You just won't have training wheels that prevent you from damaging the board. Bypassing their regulators will bypass the fixed 2V drop.