Thar be whales here!
I have often remarked on how aquatic encounters are by nature more unusual than land-based ones. Looking over the Cook Expert rules, I'm trying to remember using a whale as an encounter. This seems odd because there is actually a long history of people actively going to sea looking for these creatures.
In the rules, there are three types of whales presented: Killer (Orca), Narwhal, and Sperm whales.
(I'm too lazy to type that out)
Now, there are many more types of whales in the real world than this, but these three give a good selection to start with.
Your Killer Whale pod of 1d6 cetaceans is a frightening mid-level encounter, especially without a large vessel to keep clear of them in. They are a polar/cold water species, so a lovely iceberg-shipwreck-slash-tiny lifeboat scenario can = good times! A d20 damage is nothing to sneeze at either.
Narwhals are a bit more of a macguffin than a foe, IMO. That possibly magical horn worth 1000's of gps should motivate at least some characters to hunt them. They're tough (12HD), but skittish (Morale 8). Considering they are listed as "intelligent" among other whales (not to mention magical), it's safe to assume they'll not just blindly attack or flee without trying to do the smart thing.
Sperm whales are the juggernauts in the list. 3d20 damage (or 6d6 hull damage) but also more likely to flee than fight (Morale 7). The scariest part of the sperm whale is its swallow whole ability. Instead of succeeding on a 20, it just needs +4 over the minimum to hit. That's a lot of Jonahs!
I think whalers would be an interesting addition to a maritime campaign, or at least having them around ports and as possible ship encounters. (Ambergris as treasure, anyone?)