What Hobster said. If there's heavy rain, it washes all of the salt out of the bay, and they head for the ocean. In light rain, it doesn't matter, except for the comfort of the people in the boat.
And the opposite of what Pinstriper said, sort of. In the case of Netarts, and other estuaries that have very little in the way of streams coming in, the rain has a much lesser effect, due to less fresh water coming in.
As a general rule, if it's rained any decent amount (I don't think the last few days count), crab lower in the bay (with safety being the most important thing, always).