Berlian ferry (aka Wavemaster) had stopped operation to Harbour Bay Terminal Batam effective 13 November 2012. Reasons unknown yet. For those who still have Wavemaster tickets bought previously, you may get a refund from the terminal you purchased from.
There is currently only "Prima Ferry" that operates to Harbour Bay Batam. Their Singapore location is at the 3rd floor bridge from Harbour Front to Vivocity. Their Batam counter is 3-min walk from Harbour Bay arrival. Ask around.