Well its not so much union labor its really getting multiple regional goverment agencys to play nice with each other according to this David Sclector from Yale Law School
http://www.urbanophile.com/2015/06/22/why-are-us-rail-transit-construction-costs-so-high/
By definition, new transit rail has to run through urban areas, where property values can be valued by the square foot. If you go underground, you may have 100 years of buried pipelines, electrical stations/cables, sewer lines, etc etc that have to be identified, possibly moved. If elevated, you have NIMBYs everywhere to complain about noise and disruption unless you bribe them to find new digs.
The underground utility problem is one big factor. Contractors have to maintain a go team to mitigate an unknown utility interruption. Newark airport when building the people mover had a contractor cut into a mislabeled high voltage power feeder. The result was several days of no power to reduced power availability for much of the terminals.