I did a little research and figured out where my confusion lies. According to
this MSNBC article, the largest cruise ship in history will be constructed for Royal Caribbean. It will rise 240 feet above water level.
Mean GGB clearance is 220 feet, although at low tide it is higher. This must be what I was thinking about. This is next generation, biggest-of-the-big-scale and not what they are talking about in the original article. They clearly mean the current largest ships.
Regarding today's largest, the Queen Mary 2 is the longest at 1132 feet, but
Cruisesfun.com says the largest is the Freedom of the Seas. My guess is they are measuring by tonnage, not length, height, etc. Also, this ship is 208 feet tall and can fit "comfortably" under the GGB. So you're right viewguy, today's biggest ships can go under both bridges with no problem, pending the tides.
It was pretty exciting having the Queen Mary 2 here. Do you remember when the Port of Oakland was bringing in those huge new cranes to handle the new generation of container ships? That was amazing. They fit under the GGB by 11 feet, but only had 25 inches of clearance under the Bay Bridge. I remember they had to wait for low tide at the GGB, then wait off TI for the next low tide to squeeze under the Bay Bridge. Here's
the Chronicle's story from 2000.