Monterey is great and they devote a lot of their exhibits to the life of Monterey Bay itself, which rocks.
Went to the big Chicago aquarium a year or two ago. It was wanking! Just a thoughtless, graceless, overendowed, hypocritical pit, it was.
The San Francisco aquarium is under renovation...they moved all the sea life from the old, to-be-rebuilt site in Golden Gate Park to somewheres downtown until the rebuilding's done. I fear the New and Improved SF aquarium will mimic the Chicago aquarium, but that is an uneducated fear.
Go to Monterey. Besides the aquarium, the area offers fantastic natural history opportunities: boat trips into the bay; otters; Elkhorn Slough...