L1: PHY layer provides the maximum throughput achievable for  a given channel and PHY parameters. It could be far from the speed and user experience.

L2: MAC layer throughput tales into account the MAC overheads and inefficiencies in accessing the channel when there are a lot of nodes/CPEs communicating to an AP.

L4: Transport layer takes into account overhead of transport layer protocols, e.g. TCP.

Each one of the above measures serves a function for the designer. For user experience L4 throughput should be close to user speeds since it  takes into account overhead and delays of TCP. 

Note that even with good throughput, latency could affect user experience and thus throughput alone is not a comprehensive measure of quality of internet experience.

i think all versions of IEEE 802.11 maximum achievable throughput are either given based on measurements under ideal conditions or in the layer 2 data rates.

i hope this paper can help you..

http://www.ccs.neu.edu/home/noubir/publications/CSN.pdf

wish you the best

Physical layer, layer 2, network layer, or application layer can be used for pridiction.

Yes I know throughput can be predicted from the different layers but which of the layers gives a more dependable prediction?

L1: PHY layer provides the maximum throughput achievable for  a given channel and PHY parameters. It could be far from the speed and user experience.

L2: MAC layer throughput tales into account the MAC overheads and inefficiencies in accessing the channel when there are a lot of nodes/CPEs communicating to an AP.

L4: Transport layer takes into account overhead of transport layer protocols, e.g. TCP.

Each one of the above measures serves a function for the designer. For user experience L4 throughput should be close to user speeds since it  takes into account overhead and delays of TCP. 

Note that even with good throughput, latency could affect user experience and thus throughput alone is not a comprehensive measure of quality of internet experience.

I think if you want to measure exact throughput overall all layer should be consider. Use iperf, but as per specification Phy layer play major role in throughput improvement - if you see the 11n & 11ac spec, after that MAC.

Thanks for your answers I truly appreciate them. I am more interested in the user experience and predicting throughput from layer 4 and observing the RTT will do for now.

I will say it the Physical layer.