The waves/weather can be somewhat unpredictable so I would go for a closer marina to your destination is possible. As much as I like the boat ride being long it is no fun in the pouring rain or windy conditions. We have a relatively quick ride from GYC to Mark Island but still it can get sloppy. If we left from WAM there are many times when we would get tossed around.
If you do not reside on the islands and are only going out in good weather then it should be no concern, in that case enjoy the boat ride as Dave R said.
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