3rd will give a higher number, but of course less accurate. 4th gear is closer to a 1:1 ratio and will give the most accurate number. However if your just going for a baseline to tune with later it doesn't matter as much as long as you use that gear each time you return to the dyno.
You can ask to do All gear run. That is like running 1st thru 5 th gear. You will that the difference is minor between gears. But still you will be able to see the highest HP.
Depending on the dyno will depend on the gear. All newer version dyno's will not matter what gear you are in. We do them in 3rd gear so that the tire speed is not as high. You can do a 1st gear pull if you choose. As long as the dyno shop is not running an older version dyno( example Dyno Jet 248C or an older version of there software like WinPep 4 or 5). We have a DynoJet 248X.
