The challenge is that the whales are a quite a bit north of Seattle around the San Juan Islands. You either take a long drive (90+ minutes, not that long) and a shorter sail or a long sail. Since cars are faster the long sail option can leave you with less time near the islands. You should consider the transit time when booking. That high speed catamaran Ferry_Watcher mentioned might help solve the problem, I haven't heard much about it.
If your travels give you the option of whale watching out of Victoria BC it is much closer to the whale spotting areas.
