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The ramp at the weymouth back river is probably the best spot for accessing a few of the islands, namely Bumpkin, Grape , and Peddocks.
That being said Boston harbor most often resembles boating in a washing machine when you do it in a small boat, waves eveywhere and from every direction. You will be in for a very wet and probably uncomfortable ride in the inner harbor. Even the commuter boat wakes are difficult in a 13'. For my comfort a 17 is the smallest hull that would suffice in these waters and given the older hull design, still a bit wet.