The restaurant in Fort Point is awesome. There's a bar downstairs with some seating with a full menu and plenty of beers on tap. The second floor is mostly for reservations for dinner. There's a small patio outside (see the fencing in the picture), and they have a rooftop (again, see picture) that gets super crowded when it's nice out. They don't offer flights or anything like that, which is a shame because it's hard to resist wanting to try all of the beers when you're there. They'll usually have around 20 beers available. The food menu is slightly upscale, and everything is quite good. They do have TV's on the bottom floor, but they're only on for major events. They also offer beer to go, by the can (no need to get 4 of everything).
The Greenway Garden right in downtown Boston is where I've been the most. It's a beer garden, with a truck with 8-12 beers on tap. There's some picnic table seating and barrels for standing. It can get quite crowded, especially after-work hours. Obviously, it's only open during the warm months. It's mostly in the shade in the late afternoon, which is nice when it's extremely hot. They don't offer flights, but there's few enough beers on tap that you could probably try them all.
The Beer: This is the draw of Trillium. They're a top rated brewery in the world for a reason. They do an excellent job with IPA's, stouts, and sours. They also make a bunch of lighter options, but I usually skip those. Of the 79 beers I've had from them, I've only rated 2 below 4 Shyoh's. In fact, only 6 are below 5. Here's the spread by rating:
That brings the average to a stellar 5.30. That's incredible with that volume of different beers (for reference, the average rating on here currently is 4.556). Shout out to DDH Scaled (an IPA) as the 7.
Specifically, all the sour beers are incredible. They've got a few different series (soak/super soak, fated farmer, seesaw/double seesaw/triple seesaw) where they vary the fruit they put in it, and I will try every single one I can get my hands on. They also do slight variations of a bunch of different IPA's that are also always good. That's all without talking about the stouts, which are probably the best of the bunch. They have a bunch of 12%+ alcohol stouts that are just so so good. Hard to go wrong.
Where To Get It: The 3 open locations mentioned above. They also occasionally have it on tap at a very select group of restaurants in Boston (they're regularly at Five Horses). Really though, you just need to go to the breweries or the garden.