MTA is advising that as of Saturday, subway service has been restored between the Bronx and Brooklyn on the entire Lexington Avenue 4/5/6 route. For Brooklyn Heights, this means that 4/5 trains are again running from Borough Hall into Manhattan. See updated Hurricane Recovery map here.
In addition, MTA sent a Twitter message that the 2/3 line is also expected to return over the weekend. Of course, that links Brooklyn Heights to Manhattan at both Clark Street and Borough Hall.
Source: Brooklyn Heights Blog
http://brooklynheightsblog.com/archives/51132