You might get more info with a post in the New England Lobster Divers forum, but I'll take a shot at answering your questions.
The best sites are the ones with fewer divers, so you might want to try places where parking is difficult, like Loblolly cove.
Boat dives are generally your best bet.
Needless to say, you need to have a permit, end the dive between a half hour before and a half hour after sunset, and make sure the lobsters are legal size.
You can spearfish without a permit, but that's subject to other regulations depending on the species (no spearing striped bass is a big one). Flounder are legal as follows:
(2) Minimum Size Limits. The following minimum size limits shall apply to the catching, harvesting, landing or possession by any person of any winter flounder, fluke, dabs and gray sole.
(a) Winter Flounder: 12 inches in total length.
(b) Fluke (Summer Flounder): 14 inches in total length for commercial fishermen and 16 1/2 inches in total length for recreational fishermen.
(c) Dabs: 14 inches in total length.
(d) Gray Sole: 14 inches in total length.
(e) Windowpane Flounder: 12 inches in total length.
(from separate regulation) Yellowtail Flounder: 13 inches.
(3) Prohibitions. It is unlawful to harvest, catch. take, have on board any vessel, have in possession or land any:
(a) Winter Flounder less than 12 inches in total length.
(b) Fluke (Summer Flounder) less than 14 inches in total length for commercial fishermen and 16 1/2 inches in length for recreational fishermen.
(c) Dabs less than 14 inches in total length.
(d) Gray Sole less than 14 inches in total length.
(e) Windowpane Flounder less than 12 inches in total length.
(4) Penalties. Violation of any provision of 322 CMR 6.09 shall result in:
(a) a fine of not less than 50 nor more than $ 1,000;
(b) suspension or revocation of the commercial fisherman's permit;
(c) forfeiture of all fish unlawfully possessed;
(d) forfeiture of boats and/or fishing equipment
(including dive gear); or
(e) any combination of 322 CMR 6.09(4)(a) through (d).
Method of Measurement
(a) Minimum Size. The minimum sizes established in 322 CMR 6.03(2) shall be determined by the greatest straight line length in inches as measured on a fish with its mouth closed from the anterior most tip of the haw or snout to the farthest extremity of the tail. For fish with forked tails, the upper and lower fork may be squeezed together to measure the tail extremity.
If you need help with species identification, here's a little guide I scribbled out: