In September this year I went on two pelagics with Debi Shearwater, the first on 15/9 out of Bodega and the second on 24/9 out of Monterey. Species wise the two trips were very similar, with the Bodega Trip recording Cook's Petrel, Fork-tailed Storm-Petrel and South Polar Skua that were not seen on the Monterey trip and Ancient Murrelet and Least Storm-Petrel seen from Monterey but not Bodega.
Both trips recorded Black-footed Albatross, Pink-footed, Buller's and Sooty Shearwaters, Black, Ashy and Wilson's Storm-Petrel, Pomarine, Arctic and Long-tailed Skuas, Common and Pigeon Guillemots, Rhinocerous and Cassin's Auklets and Tufted Puffins.
Personally I preferred the Bodega pelagic as despite being full the boat was not quite as crowded, the number of most species seen was greater (150+ Long-tailed Skuas) and a better selection of Whales (Grey, Blue, Humpback and Killer v Humpack only at Monterey). The Bodega pelagic is more prone to cancellation though, so if you only have the time for one then the safer bet is Monterey, but if you can do more than one then do.