Tunnel is $6.50, although a bit under $5 with EZ-Pass. It generally only pays at night (when the Brooklyn Bridge is closed) and you don’t have the time to navigate Lower Manhattan, or if the BQE is really backed up at the tunnel split, or if you need to quickly get to the West Side. Coming into Brooklyn it pays if, again, you don’t have much time or aren’t interested in finding your way around the local streets (which can be a pain).
All other things being equal, the Brooklyn Bridge is your best option of the three (taking price into account).