Members of two locals that make up the Sheet Metal, Air and Transportation Union cast their votes Wednesday.
A labor stoppage could come on March 21 unless a contract agreement is reached or the MTA asks the White House to intervene with a second Presidential Emergency Board.
Newsday says the request for the second board would put off the strike until July at the earliest.
The MTA rejected the first board's recommendations. The agency says it remains hopeful an agreement can be reached.
Smaller LIRR unions have approved similar votes to walk off the job.
LIRR unions have been without a contract since 2010.
The railroad carries 300,000 daily commuters.