From South Station you could take the red line to Downtown Crossing or Park Street for the orange or green line. Both lines will get you to North Station. You could also walk from South Station to green or orange stops if you want some fresh air, maybe 5-10 min walk.

Used both in the past. The Acela is a shorter trip (maybe cuts an hour) and has nicer train cars than NE Regional, but I wouldn’t say it’s worth the price jump. NE is still a good way to travel, and the cars are maintained pretty well from what I remember.

Unless time is a super high priority, I’d go with NE.