I've never fished the Boston Harbor area, so I can't help you out with specifics, but I can give you some good advice nonetheless. First of all (and it's probably part of your boater's safety course) learn how to read a nautical chart and get yourself a detailed map of the area. This is invaluable and you should never be without it while on the water. A nautical chart is your roadmap and best friend. On it you can see all of the dangerous rocks and obstructions, shallow areas where you may run aground, shipping lanes you'll want to avoid, navigational bouys, and much other very useful info. Learn how to read a compass and how to navigate with a compass and chart.
If you can afford it, a GPS with chart capabilities is a great tool to have on board, and there are quite a few decently priced models on the market these days. Keep in mind that it's never wise to rely on GPS alone, as electronics have the bad habit of failing when you need them most. Always keep that chart and compass handy too.
Plan out your trip on your chart before you even get close to the water, study the chart carely so that you know the lay of the 'land' and have a good mental picture of what's out there.
ALWAYS, ALWAYS let somone know where you're going and when you'll be back, and stick to your plan. Here's what I do, as I usually am out alone, on a whim, in the middle of the night. I have a chart of my area, laminated, posted on the wall in my den. Before I go out, I always circle with a dry erase marker the area I will be in, where my truck/trailer will be parked, and write down what time I'll be back. That way if my wife wakes up the next morning and I'm not around, she can look at that and know whether or not she needs to call the Coast Guard
There is no substitute for preparation, and lack of it will always bite you in the rear. That's my 2 cents,, hope it helps and good luck out there this season!