How many voters voted for a third party candidate in the 2016 US presidential election?

A little over 6 million (out of a total of around 126 million votes cast). The final number could change slightly as absentee, provisional, and mail in ballots are counted, but it's unlikely that the percentage (around 6%) will change substantially.

Around half of those votes were for the Libertarian Party candidate, and about a fifth were for the Green Party candidate.