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I've never caught a fluke in Boston Harbor but I've heard they show up when the water is really warm. Try flounder fishing - there are lots of them out there from May to early July (and sometimes later). If your not sure where to go find the "flounder fleet" but ideally you find some softer bottom with some current nearby to fish to yourself.
There are lots of live bait opportunities in the harbor. Mackerel and harbor pollack early in the season and the pogies come in during the summer. Using live bait is the best way that I've found to get the larger bass to bite. Early morning or evening you can work the birds for smaller bass - be sure to match the hatch. It gets crowded under the birds and there are a lot of fisherman that don't show a lot of common sense when fishing under them so be careful. I've had a couple knuckle heads get too excited and gun past my lines and get tangled up with my braid.
You really can't go wrong in Boston Harbor if you take the time to learn the area.
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