There is no universal "best" or "better" in either case. It depends on your requirements. These are all valid configurations:

simulate this circuit – Schematic created using CircuitLab
These all work with N-channel MOSFETs also, and if Vcc is made negative (or if you consider Vcc to be "ground"), then they work with PNP BJTs or P-channel MOSFETs. Each has unique advantages:
The LED current in Q1's circuit is dependent only on the base voltage, and not on Vcc, and it uses only one resistor.
In Q2, \$V_{ce}\$ is only about 0.2V, giving you more available voltage for the LED and resistor than the other configurations. It also has high voltage gain, making LED current largely insensitive to input voltage (besides being on or off).
In Q3, the base current helps light the LED, the transistor doesn't saturate and so can switch faster, and it uses only one resistor.
I can't think of a lot of reasons you'd use Q4 for blinking an LED, but it does work. This arrangement is called common base, and it finds application in high frequency amplifiers.
Of course, each arrangement also suffers from unique disadvantages which I won't elaborate. Point being, the answer to your question is "it depends."
For some elaboration on some of these possibilities, see Why would one drive LEDs with a common emitter?