The Jersey City Municipal Utilities Authority (JCMUA) will handle the city’s water system for another 40 years, putting a desperately needed $50 million in the city administration’s coffers to address its messy budget problems. The contract with the autonomous city agency in charge of the city’s water and sewerage systems was approved by the Jersey City City Council Wednesday night by a 5-3 vote, with Councilmen James Solomon, Richard Boggiano and Frank Gilmore voting against the deal out of concerns about how it would affect water rates for residents. Councilwoman Amy DeGise was absent from W…