I'm planning 3+ wks in New England, traveling by public transit (no car rentals). I've visited Boston & Maine numerous times but have never been to Vermont. I like hiking, birding, exploring the coast, swimming (if water not too frigid), urban pleasures (museums, art, music, interesting vegetarian food, architecture), exploring local culture (farmers markets, music/film/art events, theater, cafés, meeting people, seeing farming, brewing, manufacturing, etc. in action).

Here's my draft itinerary so far:

T 6/12 Fly to Boston, 3 nights @ Boston Hostelling International
W 6/13-Th 6/14 Boston/Cambridge (Harvard Museums, Freedom Trail, Boston Harbor Islands? Gardner Museum? South End? ); Parker River NWR/Plum Island (train to Newburyport) then North End on way back
F 6/15 Greyhound Boston to Brattleboro VT, 1 night @ The One Cat B&B, 2 nights Latchis Hostel: Sat. farmers market; hiking? biking? Scott Farm?
M 6/18 bus to Bennington?— Bennington Museum, Potters, College etc; hiking Green Mountain NF? on to Middlebury?
Th 6/21 Bus Bennington or Middlebury to Burlington, late afternoon to evening , 3 nights Burlington Hostel
Burlington, (Shelburne?), Lake Champlain (Islands?), Mississiquoi NWR?
Sun 6/24 Megabus Burlington-Boston; overnight in Boston
M 6/25 Concord Coach Boston to Lincolnville ME, 2 nights Pine Grove Cottages Lincolnville beach, Camden Hills SP
W 6/27 Concord Coach a.m. Lincolnville to Rockland Rockland—Farnsworth Art Museum, breakwater/lighthouse, Contemporary Art Mus, ...
Th 6/28- Ferry Rockland to Vinalhaven Isle
Sun 7/1 Ferry Vinalhaven to Rockland, Concord Coach Rockland-Bangor
4 nights with family in Orono
Th 7/5 Concord Coach Bangor-Boston, overnight Boston Hostel F 7/6 Morning flight home

Here's where I'm looking for advice:
Boston: worth doing: guided Freedom Trail walk, or do on my own? Boston Harbor Islands? Activities in North End? South End? Any experiences w/public transit to Plum Island? How is June birding?
Brattleboro: recommend hiking and other activities? worthwhile eating spots?
Western Vermont by public transit: How to divide time between Bennington and Middlebury? Lower-priced lodging in either area? Access to hiking Long Trail/Green Mountain NF? Cultural highlights?
Burlington/Lake Champlain: Highlights for 2 ˝ days, staying in downtown Burlington? Best spots to visit @ Lake Champlain (Islands too?) by public transit? Shelburne Museum worth travel time and cost?
Rockland; affordable basic lodging to balance spending on more interesting places elsewhere? Worthwhile eating spots?
Vinalhaven: recommendations for hiking, bicycling, birding?
Any great birding spots in these areas that I’m missing? Any local cultural events I should know about?
I’ve had to cut out some places I really wanted to visit, either because transit unavailable or because too logistically challenging (I don’t like moving every night): in VT, Northeast Kingdom esp. Bread & Puppet Museum & St. Johnsbury; Montpelier/Barre area esp. Hope Cemetery & Rock of Ages Quarry; in ME, Belfast, Deer Isle, and Down East Coast (Machias & island/coastal refuges, Lubec, etc.). Hope I’m making the right choices, but going for a mix of active and slower-paced, relaxing days. I like to camp but for a few days here and there it doesn’t seem worth schlepping all the gear around for 3 weeks.

Thanks in advance for your input.

Wow, you are ambitious. I hope you post a trip report. Have you posted a car free trip on Chowhound. I seem to remember someone traveling in Maine without a car maybe 2 or 3 years ago.
Here's where I'm looking for advice:
Boston: worth doing: guided Freedom Trail walk, or do on my own? Boston Harbor Islands? Activities in North End? South End? Any experiences w/public transit to Plum Island? How is June birding?
It might not be in your budget but Michelle Topor's food tour of the North End is very interesting (and tasty). It's been years since we visited Boston at the right time to also visit Haymarket Square when the pushcart vendors are there on Friday and Saturday. Used to visit weekly when we worked in Boston a long time ago.
Brattleboro: recommend hiking and other activities? worthwhile eating spots?
Brattleboro Farmers Market on Saturday is great and so is the one in Norwich VT. I believe you can access Appalachian trail in Norwich. King Arthur Flour, the Norwich Farmers Market and a nice farm stand are all located on the same road. Plenty at both markets to eat. I don't think there would be much going on at an orchard in June.
Western Vermont by public transit: How to divide time between Bennington and Middlebury? Lower-priced lodging in either area? Access to hiking Long Trail/Green Mountain NF? Cultural highlights?
Burlington/Lake Champlain: Highlights for 2 ˝ days, staying in downtown Burlington? Best spots to visit @ Lake Champlain (Islands too?) by public transit? Shelburne Museum worth travel time and cost?
If you're interested in history, Shelburne Museum is wonderful. One day was enough for me but I heard other people saying they were going back for a second day. You might want to visit the Intervale and nearby Gardener's Supply near Burlington. https://www.intervale.org/ Check out website recommendations for Cycle City and birdwatching in the Intervale.
Rockland; affordable basic lodging to balance spending on more interesting places elsewhere? Worthwhile eating spots?
We loved Claws on Rt 1 north of Rockland but you mentioned vegetarian? Get list of farmers markets in Maine.
Vinalhaven: recommendations for hiking, bicycling, birding?
Any great birding spots in these areas that I’m missing? Any local cultural events I should know about?
I’ve had to cut out some places I really wanted to visit, either because transit unavailable or because too logistically challenging (I don’t like moving every night): in VT, Northeast Kingdom esp. Bread & Puppet Museum & St. Johnsbury; Montpelier/Barre area esp. Hope Cemetery & Rock of Ages Quarry; in ME, Belfast, Deer Isle, and Down East Coast (Machias & island/coastal refuges, Lubec, etc.). Hope I’m making the right choices, but going for a mix of active and slower-paced, relaxing days. I like to camp but for a few days here and there it doesn’t seem worth schlepping all the gear around for 3 weeks.
Could not find info on a boat tour we took around Deer Isle on a 4th of July visit. It was a combination of local historical society and boat captain narration so it was both history and current. One of the best boat tours we've taken. In our car, I was a little nervous about driving over the bridge to Deer Isle and turns out I was right to be worried since the bridge was designed by the same engineers at Tacoma Narrows. Was glad to hear on boat trip that modifications had been made to Deer Isle bridge so same disaster wouldn't happen. Montpelier has a nice farmers market, too.

You might get some insight into rural Vermont by reading The Town That Food Saved by Ben Hewitt. It's about the Hardwick area. You won't be in that area but I think it will help you understand the vibrancy of entrepreneurship and farming in VT. The best time to visit Maine for a cultural event would be third weekend in September for the Common Ground Fair in Unity sponsored by Organic Farmers Association.

Hope some of this information is helpful.

If you’re going to be in Boston and haven’t done it before, consider a Whale Watch. You can take a tour from the New England Aquarium. It will take you past the Harbor Islands, but not stop on them. Warning: It is colder on the water, so bring a warm sweater or jacket.

Dfrostnh, thanks for the very helpful suggestions. Some may not fit into my plans but I'm sure they'll help someone down the line.
I did not know about the Intervale Center--what a terrific tip, what an inspiring project. Even better, I'll be in Burlington during their 30th anniversary celebration. So am envisioning a day renting a bike for the Cycle the City tour, including checking out the farms, food, & music at Intervale. (Almost makes up for missing the Strolling of the Heifers in Brattleboro, 1st weekend in June; found out about that too late to take my vacation that early.) Then another day at Shelburne Museum, and checking out the rest of the city (waterfront, Church St, etc.) on the day I leave in late afternoon.
I will definitely visit the Brattleboro farmers market. Deer Isle will have to be another trip; easier to do Lincolnville, Rockland, and Vinalhaven this trip for the time I have.
I also appreciate the book recommendation.
(I've never posted on Chowhound but will see if I can find that report. And this year I'm going to try to stave off the post-vacation busy-ness enough to get up some kind of trip report.)

We spend a lot of time in VT and always have. Brattleboro is not high on our list. I would not spend all that tome there. We exit I-91 there and move on or have lunch.
Bennington, see Robert Frost’s grave if you're interested, in church graveyard.Bennington Monument. Stop at Hildene in Manchester, Robert Todd Lincoln’s summer home. Middlebury is worth much more time. See Robert Frost’s cabin up in the mountains near the college Breadloaf campus.Folklore Museum.
Burlington, yes, visit Shelbourne Farms and Shelburne Museum! Both are so worthwhile.
Burlington waterfront, Leahy Science Museum, walk the bke trail along tne Lake Champlain lakefront. Go to Church St, pedestrian street, great dining and shops. Lots of great sining in Burlinron, see UVM, The Champlain Islands give you great views of the Asirondack and Green Mts. Burlington has a wonderful Farmer’s Market on Saturdays, City Hall Park and St.Paul St.

I think you are going to find it difficult to find public transportation that will take you right to the Long Trail or to many other places in VT.

I was going to suggest renting a bike in Burlington and going out to the Intervale area but see you have already figured that option out. It is known as a good area for birding. The Ethan Allen Homestead is interesting.

If it makes you feel any better, my husband and I went to the Strolling of the Heifers for the first time last year and were a little underwhelmed.

In Boston I think you should be fine doing the Freedom Trail on your own if you pick up information explaining the various sites. I also strongly recommend spending some time on Beacon Hill and the Black Heritage Trail.

Freedom trail on your own for sure!