You generally wait the longest if you get there before it opens....and then the lines can be really long. But the lines move very quickly..and they are very organized.
if you show up later on and even very close to show time you often have no wait at all. Often there is still a wide range of shows to choose from - I would only recommend getting there really early if you are specifically waiting for only one show and you know it's selling out regularly. Otherwise don't bother.
I have gone to the TKTS booth downtown which sells tickets in advance but not sure if it was a coincidence, but the tickets I have gotten downtown have never been as good as the ones from Times Square and for the same money.